BBSRC National Bioscience Research Infrastructure: Transformative Genomics
Lead Research Organisation:
Earlham Institute
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
The National Bioscience Research Infrastructure (NBRI) in Transformative Genomics will provide scalable infrastructure to translate new advances in genomics and bioinformatics into ground-breaking discoveries innovation and market opportunities within BBSRC’s priorities. Building on the strong outcomes of the National Capability in Genomics and Single-Cell Analysis the NBRI will deliver critical support to our Institute Strategic Programmes and enable innovative research and businesses to access and exploit new technologies tools and resources at the frontiers of genomics. The NBRI will embrace technical development and translation to unlock the potential of genomes transcriptomes and epigenomes across the tree of life from individual cells to whole ecosystems ensuring that the EI and the wider UK bioscience community remain at the forefront of genomics for the benefit of society and the economy.
Planned Impact
unavailable
Organisations
- Earlham Institute (Collaboration, Lead Research Organisation)
- ROYAL BOTANIC GARDENS, KEW (Collaboration)
- ABERYSTWYTH UNIVERSITY (Collaboration)
- LANCASTER UNIVERSITY (Collaboration)
- Murdoch University (Collaboration)
- The Wellcome Trust Sanger Institute (Collaboration)
- UNIVERSITY OF MANCHESTER (Collaboration)
- University of Azores (Collaboration)
- UNIVERSITY OF EAST ANGLIA (Collaboration)
- JOHN INNES CENTRE (Collaboration)
- University of Stellenbosch (Collaboration)
- Swiss Institute of Bioinformatics (SIB) (Collaboration)
- THE PIRBRIGHT INSTITUTE (Collaboration)
- Quadram Institute Bioscience (Collaboration)
- University of Côte d'Azur (Collaboration)
- Swiss Federal Institute of Aquatic Science and Technology (Collaboration)
- MICROBIOTICA LIMITED (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- University of Sheffield (Collaboration)
- Tozer Seeds (Collaboration)
- IRCAN (Collaboration)
- University of Western Australia (Collaboration)
- Natural History museum (Collaboration)
- University of Iceland (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- UNIVERSITY OF READING (Collaboration)
- Uppsala University (Collaboration)
- UNIVERSITY COLLEGE LONDON (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- University of Antwerp (Collaboration)
- UNIVERSITY OF ESSEX (Collaboration)
- Centre for Environment, Fisheries and Aquaculture Science (Collaboration)
Publications
Aguirre-Sánchez J
(2024)
Genomic insights of S. aureus associated with bovine mastitis in a high livestock activity region of Mexico
in Journal of Veterinary Science
Al-Jourani O
(2023)
Identification of D-arabinan-degrading enzymes in mycobacteria.
in Nature communications
Avramova MM
(2023)
Global Effects of the Developmental Regulator BldB in Streptomyces venezuelae.
in Journal of bacteriology
Bell AM
(2024)
Deep sequencing of Phox2a nuclei reveals five classes of anterolateral system neurons.
in Proceedings of the National Academy of Sciences of the United States of America
Bell AM
(2023)
Deep sequencing of Phox2a nuclei reveals five classes of anterolateral system neurons.
in bioRxiv : the preprint server for biology
Bottery MJ
(2024)
Elevated mutation rates in multi-azole resistant Aspergillus fumigatus drive rapid evolution of antifungal resistance.
in Nature communications
Bowles A
(2024)
Metagenome-assembled genome of the glacier alga Ancylonema yields insights into the evolution of streptophyte life on ice and land
in New Phytologist
Caro-Castro J
(2024)
Comparative genomic analysis provides new insights into non-typhoidal Salmonella population structure in Peru.
in Scientific reports
| Description | BBSRC ALERT 2023 Assessment Panel |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | BBSRC ALERT 2024 Assessment Panel |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Anglia Innovation Partnership LLP Pre-Seed Enterprise Fund - Cell Isolation for culture QC and hyperproducer identification - Colorifix Ltd - Award Reference PSEF202301-05 |
| Amount | £11,980 (GBP) |
| Funding ID | PSEF202301-05 |
| Organisation | Norwich Research Park |
| Sector | Private |
| Country | United Kingdom |
| Start | 01/2023 |
| End | 03/2023 |
| Description | SCAnDi: Single-cell and single molecule analysis for DNA identification |
| Amount | £511,898 (GBP) |
| Funding ID | ES/Y010655/1 |
| Organisation | Economic and Social Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2024 |
| End | 03/2025 |
| Description | Targeted Long-Read Sequencing from Single Cells |
| Amount | £28,585 (GBP) |
| Organisation | Agilent Technologies |
| Sector | Private |
| Country | United States |
| Start | 05/2023 |
| End | 06/2024 |
| Title | End-to-end workflow for long-read whole-genome methylation sequencing in plants |
| Description | We developed a technical workflow to generate genome-wide DNA methylation data from plant tissue. The workflow takes flash-frozen leaf/stem tissue as an input and outputs long-read sequences ready for methylation calling, including high-molecular weight DNA extraction, ligation-mediated library preparation and long-read sequencing on the Promethion P2 Solo. The workflow is optimised to achieve sequencing Q20+ accuracies with high output. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | Too early to report on impact. |
| Title | LITE 2.0: an improved library preparation pipeline for low-cost, high-throughput whole-genome sequencing |
| Description | Low-Input Transposable Enabled (LITE) is a low-cost, short-read library preparation workflow for high-throughput processing of DNA samples from nanogram quantities. This approach, which is particularly suited for the analysis of large cohorts and population-scale studies, is widely used by EI and the wider bioscience community. We developed LITE 2.0 as a replacement for the original LITE method, incorporating both incremental and step-change improvements. The most significant improvement stems from the use of an alternative enzyme for the DNA fragmentation step, which dramatically reduces bias in regions with high GC content. LITE 2.0 is also more reproducible and amenable to higher levels of multiplexing on patterned flowcells. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | While it is too early to assess impact, LITE 2.0 is now in use at EI and accessible to the wider bioscience community through the NBRI in Transformative Genomics. |
| Title | LR scRNAseq comparative transcriptomics |
| Description | Comparison of state of the art long read sequencing approaches for single cell transcriptomic analyses : Parallel analyses of the same cDNA, generated using the 10X genomics platform, on Illumina short-read, and PacBio and Oxford Nanopore long-read platforms. We also consider the impact of CRISPR-based depletion of libraries, to remove highly expressed transcripts, prior to long-read sequencing in these experiments. |
| Type Of Material | Biological samples |
| Year Produced | 2025 |
| Provided To Others? | No |
| Impact | Comprehensive overview of experimental methods to perform long-read single-cell experiments. The aim was to treat each method using platform-specific wet lab protocols and dry lab bioinformatic data handling and processing tools to emulate a 'typical workflow' for each approach. The findings serve as a community resource for helping to select an appropriate experimental approach for isoform resolved single cell transcriptomic projects. |
| URL | https://github.com/TGAC/LR_scRNAseq_Scoones_etal |
| Description | A high-quality reference genome for Arctic charr |
| Organisation | Swiss Institute of Bioinformatics (SIB) |
| Country | Switzerland |
| Sector | Charity/Non Profit |
| PI Contribution | This collaboration forms part of the ERGA Pilot Project, established, funded, and driven entirely by a pan-European consortium of multidisciplinary scientists dedicated to generating a high-quality, complete genome for all European species. We used our expertise and infrastructure in biodiversity genomics to assemble and annotate a high-quality, annotated reference genome for the Arctic charr, a highly-adaptable fish species reared for aquaculture and an important part of the sustenance economy in Arctic and Subarctic communities. |
| Collaborator Contribution | Collaborators at the University of Iceland acted as Sample Ambassador for Arctic charr in the ERGA Pilot Project, identifying and providing the focal individual for genome assembly, contributed comparative data, and participated in the data analysis. Collaborators at the University of Antwerp generated HiC data for phasing and scaffolding. Collaborators at Wellcome Trust Sanger Institute curated the final assembly. Collaborators at Uppsala University evaluated the assembly using population genomics data. Collaborators at Uppsala University The ERGA Pilot Project is highly multi-disciplinary in nature, bringing together field biologists, ecologist, taxonomists, technical specialists and data scientists to build high-quality reference genome for biological specimens. |
| Impact | Khrystyna Kurta, Mats Pettersson, Arianna Cocco, Han Xiao, Sigurður S. Snorrason, Arnar Pálsson, Zophonías O. Jónsson, Karim Gharbi, Mariano Olivera Fedi, Kjetil Hindar, Linda Laikre, Nils Ryman and Leif Andersson. First Insights into Genetic Differentiation among Sympatric Morphs of Arctic Charr based on Whole-Genome Sequencing. 7th International Symposium on Genomics in Aquaculture (GIA2024). |
| Start Year | 2021 |
| Description | A high-quality reference genome for Arctic charr |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | This collaboration forms part of the ERGA Pilot Project, established, funded, and driven entirely by a pan-European consortium of multidisciplinary scientists dedicated to generating a high-quality, complete genome for all European species. We used our expertise and infrastructure in biodiversity genomics to assemble and annotate a high-quality, annotated reference genome for the Arctic charr, a highly-adaptable fish species reared for aquaculture and an important part of the sustenance economy in Arctic and Subarctic communities. |
| Collaborator Contribution | Collaborators at the University of Iceland acted as Sample Ambassador for Arctic charr in the ERGA Pilot Project, identifying and providing the focal individual for genome assembly, contributed comparative data, and participated in the data analysis. Collaborators at the University of Antwerp generated HiC data for phasing and scaffolding. Collaborators at Wellcome Trust Sanger Institute curated the final assembly. Collaborators at Uppsala University evaluated the assembly using population genomics data. Collaborators at Uppsala University The ERGA Pilot Project is highly multi-disciplinary in nature, bringing together field biologists, ecologist, taxonomists, technical specialists and data scientists to build high-quality reference genome for biological specimens. |
| Impact | Khrystyna Kurta, Mats Pettersson, Arianna Cocco, Han Xiao, Sigurður S. Snorrason, Arnar Pálsson, Zophonías O. Jónsson, Karim Gharbi, Mariano Olivera Fedi, Kjetil Hindar, Linda Laikre, Nils Ryman and Leif Andersson. First Insights into Genetic Differentiation among Sympatric Morphs of Arctic Charr based on Whole-Genome Sequencing. 7th International Symposium on Genomics in Aquaculture (GIA2024). |
| Start Year | 2021 |
| Description | A high-quality reference genome for Arctic charr |
| Organisation | University of Antwerp |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | This collaboration forms part of the ERGA Pilot Project, established, funded, and driven entirely by a pan-European consortium of multidisciplinary scientists dedicated to generating a high-quality, complete genome for all European species. We used our expertise and infrastructure in biodiversity genomics to assemble and annotate a high-quality, annotated reference genome for the Arctic charr, a highly-adaptable fish species reared for aquaculture and an important part of the sustenance economy in Arctic and Subarctic communities. |
| Collaborator Contribution | Collaborators at the University of Iceland acted as Sample Ambassador for Arctic charr in the ERGA Pilot Project, identifying and providing the focal individual for genome assembly, contributed comparative data, and participated in the data analysis. Collaborators at the University of Antwerp generated HiC data for phasing and scaffolding. Collaborators at Wellcome Trust Sanger Institute curated the final assembly. Collaborators at Uppsala University evaluated the assembly using population genomics data. Collaborators at Uppsala University The ERGA Pilot Project is highly multi-disciplinary in nature, bringing together field biologists, ecologist, taxonomists, technical specialists and data scientists to build high-quality reference genome for biological specimens. |
| Impact | Khrystyna Kurta, Mats Pettersson, Arianna Cocco, Han Xiao, Sigurður S. Snorrason, Arnar Pálsson, Zophonías O. Jónsson, Karim Gharbi, Mariano Olivera Fedi, Kjetil Hindar, Linda Laikre, Nils Ryman and Leif Andersson. First Insights into Genetic Differentiation among Sympatric Morphs of Arctic Charr based on Whole-Genome Sequencing. 7th International Symposium on Genomics in Aquaculture (GIA2024). |
| Start Year | 2021 |
| Description | A high-quality reference genome for Arctic charr |
| Organisation | University of Iceland |
| Country | Iceland |
| Sector | Academic/University |
| PI Contribution | This collaboration forms part of the ERGA Pilot Project, established, funded, and driven entirely by a pan-European consortium of multidisciplinary scientists dedicated to generating a high-quality, complete genome for all European species. We used our expertise and infrastructure in biodiversity genomics to assemble and annotate a high-quality, annotated reference genome for the Arctic charr, a highly-adaptable fish species reared for aquaculture and an important part of the sustenance economy in Arctic and Subarctic communities. |
| Collaborator Contribution | Collaborators at the University of Iceland acted as Sample Ambassador for Arctic charr in the ERGA Pilot Project, identifying and providing the focal individual for genome assembly, contributed comparative data, and participated in the data analysis. Collaborators at the University of Antwerp generated HiC data for phasing and scaffolding. Collaborators at Wellcome Trust Sanger Institute curated the final assembly. Collaborators at Uppsala University evaluated the assembly using population genomics data. Collaborators at Uppsala University The ERGA Pilot Project is highly multi-disciplinary in nature, bringing together field biologists, ecologist, taxonomists, technical specialists and data scientists to build high-quality reference genome for biological specimens. |
| Impact | Khrystyna Kurta, Mats Pettersson, Arianna Cocco, Han Xiao, Sigurður S. Snorrason, Arnar Pálsson, Zophonías O. Jónsson, Karim Gharbi, Mariano Olivera Fedi, Kjetil Hindar, Linda Laikre, Nils Ryman and Leif Andersson. First Insights into Genetic Differentiation among Sympatric Morphs of Arctic Charr based on Whole-Genome Sequencing. 7th International Symposium on Genomics in Aquaculture (GIA2024). |
| Start Year | 2021 |
| Description | A high-quality reference genome for Arctic charr |
| Organisation | Uppsala University |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | This collaboration forms part of the ERGA Pilot Project, established, funded, and driven entirely by a pan-European consortium of multidisciplinary scientists dedicated to generating a high-quality, complete genome for all European species. We used our expertise and infrastructure in biodiversity genomics to assemble and annotate a high-quality, annotated reference genome for the Arctic charr, a highly-adaptable fish species reared for aquaculture and an important part of the sustenance economy in Arctic and Subarctic communities. |
| Collaborator Contribution | Collaborators at the University of Iceland acted as Sample Ambassador for Arctic charr in the ERGA Pilot Project, identifying and providing the focal individual for genome assembly, contributed comparative data, and participated in the data analysis. Collaborators at the University of Antwerp generated HiC data for phasing and scaffolding. Collaborators at Wellcome Trust Sanger Institute curated the final assembly. Collaborators at Uppsala University evaluated the assembly using population genomics data. Collaborators at Uppsala University The ERGA Pilot Project is highly multi-disciplinary in nature, bringing together field biologists, ecologist, taxonomists, technical specialists and data scientists to build high-quality reference genome for biological specimens. |
| Impact | Khrystyna Kurta, Mats Pettersson, Arianna Cocco, Han Xiao, Sigurður S. Snorrason, Arnar Pálsson, Zophonías O. Jónsson, Karim Gharbi, Mariano Olivera Fedi, Kjetil Hindar, Linda Laikre, Nils Ryman and Leif Andersson. First Insights into Genetic Differentiation among Sympatric Morphs of Arctic Charr based on Whole-Genome Sequencing. 7th International Symposium on Genomics in Aquaculture (GIA2024). |
| Start Year | 2021 |
| Description | A high-quality reference genome for Cardamine caldeirarum |
| Organisation | University of Azores |
| Country | Portugal |
| Sector | Academic/University |
| PI Contribution | We used our expertise and infrastructure in biodiversity genomics to assemble and annotate a high-quality, annotated reference genome for Cardamine caldeirarum, a watercress species endemic to the Azores archipelago. |
| Collaborator Contribution | Collaborators at the University of the Azores sourced the plant material for genome assembly and annotation. |
| Impact | Knowledge exchange: short visit by collaborator to learn about high-molecular weight DNA extraction and long-read sequencing. |
| Start Year | 2023 |
| Description | ENQ-3404 |
| Organisation | Lancaster University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transcriptomic data generation of C.elegans samples |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptomic resources for understanding biological variation in C. elegans |
| Start Year | 2023 |
| Description | ENQ-4958 |
| Organisation | University of Manchester |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Metabarcoding data generation of environmental samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resource to classify and characterise microbial communities in soil |
| Start Year | 2023 |
| Description | ENQ-5115 |
| Organisation | University of Reading |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of environmental soil samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resource to classify and characterise microbial communities in ancient soil |
| Start Year | 2023 |
| Description | ENQ-5307 |
| Organisation | Swiss Federal Institute of Aquatic Science and Technology |
| Country | Switzerland |
| Sector | Public |
| PI Contribution | Genome data generation of E. coli samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand E. coli genomes |
| Start Year | 2023 |
| Description | ENQ-5318-A |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of beetle samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand beetle genomes |
| Start Year | 2023 |
| Description | ENQ-5318-B |
| Organisation | Natural History Museum |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Genome data generation of beetle samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand beetle genomes |
| Start Year | 2023 |
| Description | ENQ-5398 |
| Organisation | University of Stellenbosch |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | Genome data generation of human samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand human genomics. |
| Start Year | 2024 |
| Description | ENQ-5440 |
| Organisation | University of Edinburgh |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of fruit fly samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand fruit fly genomes |
| Start Year | 2023 |
| Description | ENQ-5447 |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of Zebrafish samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand variation in zebrafish. |
| Start Year | 2024 |
| Description | ENQ-5459 |
| Organisation | The Pirbright Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of chicken samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to identify, characterise and understand variants in chicken genomes |
| Start Year | 2023 |
| Description | ENQ-5461 |
| Organisation | The Pirbright Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transcriptomic data generation of cow cDNA samples |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptomic resources for understanding biological variation in Bos taurus |
| Start Year | 2023 |
| Description | ENQ-5466 |
| Organisation | University of Nottingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Annotation of wheat genomes |
| Collaborator Contribution | Provision of materials |
| Impact | Annotated genome resource to characterise and understand wheat genomes |
| Start Year | 2023 |
| Description | ENQ-5467 |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of Brassica samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand Brassica varieties. |
| Start Year | 2024 |
| Description | ENQ-5507 |
| Organisation | University of Essex |
| Country | United Kingdom |
| PI Contribution | Metabarcoding data generation of environmental samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resource to classify and characterise microbial communities |
| Start Year | 2023 |
| Description | ENQ-5561 |
| Organisation | University of Côte d'Azur |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Genome data generation of yeast samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand yeast genomes |
| Start Year | 2023 |
| Description | ENQ-5569 |
| Organisation | Aberystwyth University |
| Department | Institute of Biological, Environmental and Rural Sciences (IBERS) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transcriptomic data generation of Mischanthus samples |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptomic resources for understanding biological variation in Mischanthus |
| Start Year | 2023 |
| Description | ENQ-5660-A |
| Organisation | University of Western Australia |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Genome data generation of wheat samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand wheat genomes |
| Start Year | 2023 |
| Description | ENQ-5660-B |
| Organisation | Murdoch University |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Genome data generation of wheat samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand wheat genomes |
| Start Year | 2023 |
| Description | ENQ-5662 |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of pea samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand pea genomes |
| Start Year | 2023 |
| Description | ENQ-5807 |
| Organisation | University of Edinburgh |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of Trypanosoma samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Resources to better understand trypanosoma genomes. |
| Start Year | 2024 |
| Description | ENQ-5820 |
| Organisation | IRCAN |
| Country | France |
| Sector | Charity/Non Profit |
| PI Contribution | Genome data generation of yeast samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand yeast |
| Start Year | 2024 |
| Description | ENQ-5845 |
| Organisation | The Pirbright Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Trancriptomic data generation of Infectious Bronchitis virus/Gallus gallus samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptomic resources for understanding infection response in chicken. |
| Start Year | 2024 |
| Description | ENQ-5912 |
| Organisation | University College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation from Human single-cell DNA samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand human genomics. |
| Start Year | 2024 |
| Description | ENQ-5936 |
| Organisation | University of Sheffield |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of Streptococcus samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and better understand variation in Group A Streptococcus. |
| Start Year | 2024 |
| Description | ENQ-5949 |
| Organisation | Centre For Environment, Fisheries And Aquaculture Science |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Metabarcoding data generation of environmental samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resource to classify and characterise marine communities |
| Start Year | 2024 |
| Description | ENQ-5955 |
| Organisation | Quadram Institute Bioscience |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of viral metagenome samples from human gut |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand viral genomics in the human gut. |
| Start Year | 2024 |
| Description | ENQ-5956 |
| Organisation | University College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation from Human single-cell DNA samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand human genomics. |
| Start Year | 2024 |
| Description | ENQ-5986 |
| Organisation | University College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation from Human single-cell DNA samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand human genomics |
| Start Year | 2024 |
| Description | ENQ-6011 |
| Organisation | IRCAN |
| Country | France |
| Sector | Charity/Non Profit |
| PI Contribution | Genome data generation of yeast samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand yeast |
| Start Year | 2024 |
| Description | ENQ-6013 |
| Organisation | University of Edinburgh |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of Drosophila samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand variation in Drosophila. |
| Start Year | 2024 |
| Description | ENQ-6062 |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of Beetle samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand beetle genomics. |
| Start Year | 2024 |
| Description | New industry partner supporting DTP studentship |
| Organisation | Microbiotica Limited |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | DTP studentship of YB was converted to CASE due to involvement of industry partner. |
| Collaborator Contribution | provide intellectual input, access to microbiome samples and anaerobic culturing facilities |
| Impact | This collaboration is multi-disciplinary Industry partner - expertise in culturing anaerobic bacteria EI - Single cell and microfluidics isolation workflows |
| Start Year | 2023 |
| Description | PDEV-89 HiDEF-seq |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Technical Genomics (script to identify restriction enzyme,s lab work and sequencing). |
| Collaborator Contribution | Neil Hall (funding and data analysis) |
| Impact | Creation of an R pipeline to identify restriction enzyme for HiDEF-seq |
| Start Year | 2024 |
| Description | Study of the genomic architecture and domestication history of black fonio (Digitaria iburua) |
| Organisation | Royal Botanic Gardens, Kew |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We are using our expertise and infrastructure in biodiversity genomics to generate data for the assembly of high-quality reference genome for black fonio (Digitaria iburua), a millet species cultivated in West Africa. |
| Collaborator Contribution | Collaborators at Kew Gardens secured the plant material for genome assembly. |
| Impact | Too early to report outcomes. |
| Start Year | 2024 |
| Description | Tozer Seeds Knowledge Transfer Partnership |
| Organisation | Tozer Seeds |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Develop a project idea for a Knowledge Transfer Partnership (KTP) with Tozer Seeds, management of the application process and negotiation of IP and terms. The KTP will help Tozer to develop internal capacity to analyse genomic data for accelerated breeding. This collaboration began as a service provided by NBRI1 and JV in 2022, after which the BDI team assisted in developing it further into the KTP. |
| Collaborator Contribution | Tozer co-applied for KTP with EI and will be providing funding and in-kind support. |
| Impact | Application for a KTP submitted in November 2023. Earlham Institute gaining status as a KTN Knowledge Base. KTP was funded and started in July 2024 and will run till December 2026 (30 months) |
| Start Year | 2022 |
| Title | D-Mag: Data Management release v1.2.0 |
| Description | D-Mag is a tool designed to streamline data management across EI's internal data storage locations (raw, qc, private_reads, /ei/cb/) managed by the Core Bioinformatics and Genomic Pipelines groups. A file usage report is generated for each storage location through a regular cron job that runs the disk utility (du) program. D-Mag utilises the file usage report and also pulls metadata from JIRA and then generates a review list of folders with modification dates older than a specified range. This review list can be edited to update the status of directories, marking them for deletion or retention (open, keep). Subsequently, D-Mag processes the reviewed list, creating a record of status changes, deleting the necessary directories, logging their content and posting updates to JIRA. This utility assists in managing data locations across these areas, ensuring storage of any new data generated by Next-Generation sequencing and subsequent data analysis. ** Main changes added to this release ** - Fixed JIRA post text rendering 45a743b - Updated post_text_comment_to_jira c4b50d2 - Updated JIRA Quote reference and Date project completed customfields 7e4a6e7 - Updated check_pip_is_valid subroutine 64149c1 - Updated JIRA Epic_Name, Primary_Contact_Name, Primary_email_address customfields 0771041 - Added new JIRA Cloud API url e716ed8 - Updated DO_NOT_DELETE hash 2dcbf40 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | D-Mag is a tool designed to streamline data management across EI's internal data storage locations (raw, qc, private_reads, /ei/cb/) managed by the Core Bioinformatics and Genomic Pipelines groups. This utility assists in managing data locations across these areas, ensuring storage of any new data generated by Next-Generation sequencing and subsequent data analysis. |
| URL | https://github.com/EI-CoreBioinformatics/D-Mag |
| Title | D-Mag: Data Management release v1.2.1 |
| Description | D-Mag is a tool designed to streamline data management across EI's internal data storage locations (raw, qc, private_reads, /ei/cb/) managed by the Core Bioinformatics and Genomic Pipelines groups. A file usage report is generated for each storage location through a regular cron job that runs the disk utility (du) program. D-Mag utilises the file usage report and also pulls metadata from JIRA and then generates a review list of folders with modification dates older than a specified range. This review list can be edited to update the status of directories, marking them for deletion or retention (open, keep). Subsequently, D-Mag processes the reviewed list, creating a record of status changes, deleting the necessary directories, logging their content and posting updates to JIRA. This utility assists in managing data locations across these areas, ensuring storage of any new data generated by Next-Generation sequencing and subsequent data analysis. ** Main changes added to this release ** - Added new PAP JIRA email address to reflect JIRA upgrade 98a0d56 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | D-Mag is a tool designed to streamline data management across EI's internal data storage locations (raw, qc, private_reads, /ei/cb/) managed by the Core Bioinformatics and Genomic Pipelines groups. This utility assists in managing data locations across these areas, ensuring storage of any new data generated by Next-Generation sequencing and subsequent data analysis. |
| URL | https://github.com/EI-CoreBioinformatics/D-Mag |
| Title | D-Mag: Data Management release v1.2.2 |
| Description | D-Mag is a tool designed to streamline data management across EI's internal data storage locations (raw, qc, private_reads, /ei/cb/) managed by the Core Bioinformatics and Genomic Pipelines groups. A file usage report is generated for each storage location through a regular cron job that runs the disk utility (du) program. D-Mag utilises the file usage report and also pulls metadata from JIRA and then generates a review list of folders with modification dates older than a specified range. This review list can be edited to update the status of directories, marking them for deletion or retention (open, keep). Subsequently, D-Mag processes the reviewed list, creating a record of status changes, deleting the necessary directories, logging their content and posting updates to JIRA. This utility assists in managing data locations across these areas, ensuring storage of any new data generated by Next-Generation sequencing and subsequent data analysis. ** Main changes added to this release ** - Updated regular expression to target string in the format '73.21T total' 61027d4 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | D-Mag is a tool designed to streamline data management across EI's internal data storage locations (raw, qc, private_reads, /ei/cb/) managed by the Core Bioinformatics and Genomic Pipelines groups. This utility assists in managing data locations across these areas, ensuring storage of any new data generated by Next-Generation sequencing and subsequent data analysis. |
| URL | https://github.com/EI-CoreBioinformatics/D-Mag |
| Title | D-Mag: Data Management release v1.3.0 |
| Description | D-Mag is a tool designed to streamline data management across EI's internal data storage locations (raw, qc, private_reads, /ei/cb/) managed by the Core Bioinformatics and Genomic Pipelines groups. A file usage report is generated for each storage location through a regular cron job that runs the disk utility (du) program. D-Mag utilises the file usage report and also pulls metadata from JIRA and then generates a review list of folders with modification dates older than a specified range. This review list can be edited to update the status of directories, marking them for deletion or retention (open, keep). Subsequently, D-Mag processes the reviewed list, creating a record of status changes, deleting the necessary directories, logging their content and posting updates to JIRA. This utility assists in managing data locations across these areas, ensuring storage of any new data generated by Next-Generation sequencing and subsequent data analysis. ** Main changes added to this release ** - Added PacBio Revio files to archive list 648597d - Enabled check on run folder name date during dry run 6a500ad - Updated PacBio run folder with a new format 8ba751b - Added option --recheck_days and available to command line 84e0893 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | D-Mag is a tool designed to streamline data management across EI's internal data storage locations (raw, qc, private_reads, /ei/cb/) managed by the Core Bioinformatics and Genomic Pipelines groups. This utility assists in managing data locations across these areas, ensuring storage of any new data generated by Next-Generation sequencing and subsequent data analysis. |
| URL | https://github.com/EI-CoreBioinformatics/D-Mag |
| Title | D-Mag: Data Management release v1.4.0 |
| Description | D-Mag is a tool designed to streamline data management across EI's internal data storage locations (raw, qc, private_reads, /ei/cb/) managed by the Core Bioinformatics and Genomic Pipelines groups. A file usage report is generated for each storage location through a regular cron job that runs the disk utility (du) program. D-Mag utilises the file usage report and also pulls metadata from JIRA and then generates a review list of folders with modification dates older than a specified range. This review list can be edited to update the status of directories, marking them for deletion or retention (open, keep). Subsequently, D-Mag processes the reviewed list, creating a record of status changes, deleting the necessary directories, logging their content and posting updates to JIRA. This utility assists in managing data locations across these areas, ensuring storage of any new data generated by Next-Generation sequencing and subsequent data analysis. ** Main changes added to this release ** - The release was to make D-Mag integrate with the new Krono cluster - The update removed the Perl MIME::Lite library and instead used curl to send email for the new Kronos cluster 7e96841 - Updated the HPC Perl installation to make use of the updated Perl libraries (perl-5.32.1_kronos_CBG) |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | D-Mag is a tool designed to streamline data management across EI's internal data storage locations (raw, qc, private_reads, /ei/cb/) managed by the Core Bioinformatics and Genomic Pipelines groups. This utility assists in managing data locations across these areas, ensuring storage of any new data generated by Next-Generation sequencing and subsequent data analysis. |
| URL | https://github.com/EI-CoreBioinformatics/D-Mag |
| Title | D-Mag: Data Management release v2.0.0 |
| Description | D-Mag is a tool designed to streamline data management across EI's internal data storage locations (raw, qc, private_reads, /ei/cb/) managed by the Core Bioinformatics and Genomic Pipelines groups. A file usage report is generated for each storage location through a regular cron job that runs the disk utility (du) program. D-Mag utilises the file usage report and also pulls metadata from JIRA and then generates a review list of folders with modification dates older than a specified range. This review list can be edited to update the status of directories, marking them for deletion or retention (open, keep). Subsequently, D-Mag processes the reviewed list, creating a record of status changes, deleting the necessary directories, logging their content and posting updates to JIRA. This utility assists in managing data locations across these areas, ensuring storage of any new data generated by Next-Generation sequencing and subsequent data analysis. ** Main changes added to this release ** - Created a Python package for the tool - Created a new script to search JIRA projects for identifying the run status (PSEQ ticket and Project status) and add these details to the output file using JIRA API - Added GitHub actions to create releases |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | D-Mag is a tool designed to streamline data management across EI's internal data storage locations (raw, qc, private_reads, /ei/cb/) managed by the Core Bioinformatics and Genomic Pipelines groups. This utility assists in managing data locations across these areas, ensuring storage of any new data generated by Next-Generation sequencing and subsequent data analysis. |
| URL | https://github.com/EI-CoreBioinformatics/D-Mag |
| Title | EI Functional Annotation Pipeline (eifunannot) release v1.4.0 |
| Description | The EI Functional Annotation Pipeline (eifunannot) is a Python3 and Snakemake-based workflow designed to streamline functional annotation tasks. It integrates various functional annotation tools, including AHRD, InterProScan, and BLAST, consolidating their results into an integrated summary TSV file. Additionally, eifunannot generates individual output files from these tools, facilitating both internal and external functional annotation projects. This automated pipeline enhances project delivery efficiency through easily configurable configuration files. ** Main changes added to this release ** - Added new download_from_uniprot script by which download Uniprot database as well as exclude a taxon id, add manually curated isoforms, and filter database for incomplete sequences 17d0796, e03608f, a7e3c64 - Added feature to exclude HPC nodes - cluster_config.json 798c198 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The eifunannot pipeline is essential for producing functional annotations for gene predictions, thereby improving the quality of genome annotation projects conducted internally for our research faculty, as well as for external researchers and collaborators. Furthermore, it has been employed as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eifunannot |
| Title | EI Functional Annotation Pipeline (eifunannot) release v1.5.0 |
| Description | The EI Functional Annotation Pipeline (eifunannot) is a Python3 and Snakemake-based workflow designed to streamline functional annotation tasks. It integrates various functional annotation tools, including AHRD, InterProScan, and BLAST, consolidating their results into an integrated summary TSV file. Additionally, eifunannot generates individual output files from these tools, facilitating both internal and external functional annotation projects. This automated pipeline enhances project delivery efficiency through easily configurable configuration files. ** Main changes added to this release ** ## Features - Added new scripts added for internal functional annotation releases - Added script to parse tabular blast output - parse_blast.py 249e518 - Added script to create functional annotation summary file - create_functional_annotation.py 249e518 - Added script to add functional description to release GFF3 - add_description_to_annotation_GFF3.py 7a3233b - Added --keep-going option to enable run of independent jobs if a job fails 14f826a - Updated run config to use /ei/public location to use the resources sitewide be2fe2f - Increased default number of cluster jobs to 200 3de13c2 - Updated cluster config f74c92e |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The eifunannot pipeline is essential for producing functional annotations for gene predictions, thereby improving the quality of genome annotation projects conducted internally for our research faculty, as well as for external researchers and collaborators. Furthermore, it has been employed as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eifunannot |
| Title | EI Functional Annotation Pipeline (eifunannot) release v1.5.1 |
| Description | The EI Functional Annotation Pipeline (eifunannot) is a Python3 and Snakemake-based workflow designed to streamline functional annotation tasks. It integrates various functional annotation tools, including AHRD, InterProScan, and BLAST, consolidating their results into an integrated summary TSV file. Additionally, eifunannot generates individual output files from these tools, facilitating both internal and external functional annotation projects. This automated pipeline enhances project delivery efficiency through easily configurable configuration files. ** Main changes added to this release ** ## Features - Remove SFLD hits support due to an update to kronos cluster 25bc78c - Updated cluster configuration to work on the updated kronos cluster 9677f8d |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The eifunannot pipeline is essential for producing functional annotations for gene predictions, thereby improving the quality of genome annotation projects conducted internally for our research faculty, as well as for external researchers and collaborators. Furthermore, it has been employed as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eifunannot |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v1.5.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Added support for SMRT Link v11.1.0.166339 - Added new PAP Jira email address as part of JIRA Cloud upgrade bb60b65 - Updated README.md 496fca7, 6627ff2 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v1.6.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Stable release using PacBio SMRT Link v11.1.0.166339 - IsoSeq3 pipeline, isoseq3, is still using an earlier version of PacBio SMRT Link v10.2.0.133434 - demux_ccs pipeline: added a few more header variables to remove the header line from barcode CSV input. There are still a few characters not encoded correctly b4cef9f - Changed pipeline name isoseq3_teloprime -> isoseq3_nobarcode a64e790 - Changed pipeline name ccs_demux -> demux_ccs 31f25bf - Updated pb_isoseq3 and pb_isoseq3_nobarcode pipelines to work with hifi_reads input but using SMRT link v10.2.0.133434 as the new v11.1.0.166339 is having errors at call-refine stage. The error is reported to PacBio Dev Team 827eec0 - Updated demux_ccs pipeline to SMRT link v11.1.0.166339 7a47a78 - Removed --relative option for rule generate_barcodeset_xml bb79f91 - Get absolute path for input --primers_fasta 3fd17da - Only add barcode CSV and barcode fasta to reads location with --copy_raw d0adb76 - Added support for reads.bam, hifi_reads.bam and hifi_read.bam with kinetics - Updated copy_raw, run_qc pipelines cbd8271 - Removed subreadset.xml support 6b82c55 - Added new pacbio_instrument format 'hifi_reads_kinetics_bam' fbfe677 - Added 5mC CpG Report to Run-QC PDF report 982dcd4 - Updated raw reads readme PDF report to support reads.bam, hifi_reads.bam and hifi_reads.bam (with kinetics) 77976cc - Added --keep-going option to enable run of independent jobs if a job fails 06ba867 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v1.7.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Stable release using PacBio SMRT Link v12.0.0.177059 68b6df7 - Updated PacBio Run-QC report to SMRT Link v12.0.0.177059 b74fed6 - Updated Demultiplex Barcodes pipeline to SMRT Link v12.0.0.177059 e96532a - Added script to format barcode CSV files - format_barcode_csv.py f5799f6 - Removed BOM (\ufeff) from barcode CSV file - format_barcode_csv.py 01abcdb - Added feature to exclude HPC nodes d2380de - IsoSeq3 pipeline, isoseq3, is still using an earlier version of PacBio SMRT Link v10.2.0.133434 - Added sleep 180 to allow very low-depth SMRT cell reads to appear on disk (latency) 3fb1ddf - Create a data package directory to prevent the 'No such file or directory' error when 'copy_raw' rule finishes quickly c1490cb - Formated table description when encountering medium set (>8) of barcoded data 4617261 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v2.0.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - PacBio Revio Support Release using PacBio SMRT Link v12.0.0.177059 - format_pacbio_samplesheet script creates the project title in the same format as the create_project_directory script. So the --title option is not necessary with format_pacbio_samplesheet - Added new scripts - create_project_directory, parse_json |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v2.1.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - PacBio Revio Support Release using PacBio SMRT Link v12.0.0.177059 - Extracts barcodes for all unique barcodes, i.e., even asymmetric barcodes 7ad9042 - Removed required PacBio Revio raw file 'nvidia-smi.log' to optional 8c5364e - Added rule recreate_raw_revio_output to rule create_revio_data_report if we do pb_undo_demux to fix tar error 'file changed as we read it' 12a8345 - Removed required input for --raw_reads_output option in eipacbiopap configure command da56ca1 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v2.2.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - PacBio Revio Support Release using PacBio SMRT Link v12.0.0.177059 - Added new PacBio CSP logo for reports ce77653 - Added feature to post to JIRA with a warning 8397070 - Updated pipeline to notify JIRA when lima demultiplexed barcodes do not match between hifi_reads and fail_reads for Revio runs (PPBFX-1203) e0a2989 - Updated rule to notify JIRA when recreating Revio output files 13bb2a8 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v3.0.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Updated pipeline to SMRT Link v13 release - Added new rule to post CCS report stats to JIRA using the new jira_plugin.py script d9d938f - Added new JIRA plugin script ed82b1e - tar raw reads for projects marked 'joint' as default since we are generating more of HiFi reads 98e0da9 - Removed the clean up on fail_reads.consensusreadset.xml for non-existent files 2de0518 - Removed software from testing env a366e02 - pb_isoseq3 is now pb_isoseq in v13.0.0.207600 5bd007a - Removed pb_undo_demux (--undo_demux) support for PacBio Revio until we get test data to work with cbd9f77 - Increased memory of packaging jobs 1783023 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v3.1.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Updated pipeline to support SMRT Link v13 IsoSeq analysis - Updated script to rename isoseq output files (both single/multi-plex and with/without clustering) for SMRT Link v13 release e15ffc3 - Updated IsoSeq PDF report script for v13 1ae7ed2, a247f20, 6ef85fb, fcc8c92 - Added new location to store secondary analysis data package output to eipacbiopap configure (--analysis_output) 4660f46, 842a8bf - Copy of raw Revio reads (--copy_raw) without barcoded data implemented 0048abc - Added new rule copy_barcodes to copy Revio barcodes information (fasta and CSV) to raw output 'metadata' folder when using --copy_raw option 4bf8f0e - Added rule pbreports_report_barcode as a dependency for rule create_revio_data_report when run with just --copy_raw for Revio fc325e8 - Disabled processing of demultiplexed raw Revio SMRT cell input until we get the data to test undo demux or any other analysis downstream 12fd93e - Disabled --copy_raw if --pipeline demux_ccs provided and update help docs e8c83c4 - Added checks to count the barcodes we extract and add --force option to overwrite - extract_barcode_fasta.py 58b1846 - For PacBio Revio data, only run copy_raw rules when requested and always for pb_demux_ccs pipeline 8de9b62 - Keep analysis folder in the data package folder and not delete them c1a52ae - HPC exclude option can be left blank. The new format to exclude HPC nodes is - 'exclude': '--exclude=t128n[30,41]', in the hpc_config.json 2ef1339 - Increased default isoseq jobs memory 67860ed - Exit configure if no '--copy_raw' or '--pipeline' option provided da198a2 - Exit configure if non-tested pipeline 'isoseq_nobarcode' is given 643cc30 - Move backup of barcodes and CSV under PPBFX title location a26e845 - Added example output format for reference adf991f - Move isoseq analysis snakemake done files to /ei/cb/analysis/PPBFX location 6aaec45 - Adjusted barcode fasta and csv lookup under PPBFX folder as external data package is tarred and folder is deleted afterwards 39d1586 - Fixed broken link to SMRT Link user guide ecc25f9 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v3.2.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Updated pipeline to support SMRT Link v13 Read Segmentation and Single-Cell IsoSeq analysis - Configured --copy_raw to package raw reads for pb_segment_reads_and_sc_isoseq without barcodes_csv 9458477 - Added read segmentation and single-cell iso-Seq analysis specific files d720be2 - Updated configure script to incorporate pb_segment_reads_and_sc_isoseq pipeline 6171bf1 - Updated run_config.yaml for pb_segment_reads_and_sc_isoseq pipeline bab9c13 - Added new script for Read Segmentation and Single-Cell IsoSeq PDF report, thanks @yuxuanlan for initial help 12d86af - Completed support for the Read Segmentation and Single-Cell IsoSeq analysis ef58a58 - Updated hpc_config.json for rules pb_segment_reads_and_sc_isoseq and pack_pb_segment_reads_and_sc_isoseq dfbec3b |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v4.0.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - BREAKING CHANGE - Updated smrtlink-13.0.0.207600 to smrtlink-13.1.0.221970 4e2a964 - Fixed issue with Revio SMRT link v13.1 where the raw SMRT cell does not contail *fail_reads.consensusreadset.xml 0392f0e - Added JIRA field as required for eipacbiopap configure command and added steps to create fail reads XML as part of configure command e7615a9 - Updated create_pdf_report_pacbio_revio_data_report.pl script to v13.1 changes fce9c4a - Updated recreate_raw_revio_output.py script for v13.1 changes - add full_preview_29hr files, adapt to new demultiplex output format ie - movie.hifi_reads.barcode.bam format instead of movie.barcode.bam format b50423c - Isolated trigger for rule pb_segment_reads_and_sc_isoseq to run as per configure 3e7101d - Updated pipeline parameters and cromwell_config files for v13.1 f66cbac - Changed default barcodes and primers for v13.1 69a4d39 - Updated HPC memory for rule recreate_raw_revio_output to overcome HPC memory issues with rsync/cp commands fb065de - Removed pre-existing link used for testing pb_segment_reads_and_sc_isoseq f35010b |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v4.1.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Added feature to enable raw reads packaging (--copy_raw) with or without providing barcodes (--barcode_csv) 68d396e - Added a new threshold percentage for demultiplexed HiFi Reads count to trigger a warning to be reported to JIRA for capturing incorrect barcode issues (--demultiplexed_hifi_reads_threshold) 1a68aea - Moved Revio Data Report PDF to project folder 8fccfcb - Added debug option for recreate_raw_revio_output.py e20828f |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v4.2.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Added ability to run Read Segmentation and Single-Cell IsoSeq pipeline after demultiplexing - Added new script generate_mock_barcode_run_folders to create a mock per barcode run folders for running pb_segment_reads_and_sc_isoseq pipeline 85caa05 - Updated pacbio_segment_reads_and_sc_isoseq PDF report to SMRT Link v13.1 release 013e87c - Standardised backup PDF report locations across pipelines 70a5027 - Fixed package name for pb_segment_reads_and_sc_isoseq pipeline 6058fb2 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v4.2.1 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Only report lima guess 'Picked' barcodes to JIRA if missed from input barcodes CSV 2f186d4 - Fixed incorrect table reference when processing TSV f2021d2 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v4.3.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Added ability to run Read Segmentation and Single-Cell IsoSeq pipeline after combining demultiplexed data from multiple SMRT cells - Updated snakemake to support the new pipeline 'isoseq_with_mapping' 38c1270 - Added new script to create PDF report for IsoSeq with Mapping pipeline 'isoseq_with_mapping' - create_pdf_report_pacbio_isoseq_with_mapping.pl 8136d33 - Updated default hpc_config.json to support the new pipeline 'isoseq_with_mapping' 5a6cc99 - Updated default run_config.yaml to support the new pipeline 'isoseq_with_mapping' 453536f - Updated eipacbiopap configure to support the new pipeline 'isoseq_with_mapping' 1448185 - Updated isoseq pipeline PDF report for SMRT Link v13.1 release 19212ef - Added new script to create per barcode run folders for pb_segment_reads_and_sc_isoseq pipeline from TSV file - generate_mock_run_folders_from_tsv.py. Make sure to run --pipeline pb_segment_reads_and_sc_isoseq pipeline by excluding --copy_raw option using the samplesheet generated from running this script 59de9ef - Added new option --isoseq to add isoseq specific '5p' and '3p' tags to barcode names in format_barcode_csv.py script d4e937e - Removed the requirement to provide a title from command-line for eipacbiopap configure command and use the package_name from the samplesheet instead fa781cc |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v4.3.1 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Added ei-pap queue to the list of HPC job queues 10817c6 - Removed old tgac-pap queue partition name to ei-pap 41d9825 - Added missing JIRA summary for 'isoseq_with_mapping' pipeline 309837c - Fixed figure description numbering for 'isoseq_with_mapping' PDF report bc7e56c |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v4.4.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Added ability to run Read Segmentation and IsoSeq pipeline after combining demultiplexed data from multiple SMRT cells - Updated eipacbiopap configure to support pb_segment_reads_and_isoseq pipeline e7c61ba - Updated run_config.yaml and hpc_config.json for pb_segment_reads_and_isoseq ed419af - Updated snakemake to support new Read Segmentation and IsoSeq pipeline pb_segment_reads_and_isoseq 26a988c - Updated reporting summary to JIRA for Read Segmentation and IsoSeq pipeline 9cb9e4e - Added new script for Read Segmentation and IsoSeq PDF report bfbdac8 - Added new script to rename PacBio Read Segmentation and IsoSeq output to actual sample names when packaging data 7a6bc6e - Added new option to enable custom --tag to output file name for format_barcode_csv script, to differentiate normal barcode from other (kinnex, for example) barcodes d8e758d - Updated jira_plugin.py by adding feature to attach files to JIRA 029287c - Fixed incorrect percentage reporting on read_segmentation_report_attribute values a10c1b8 - Fixed get cluster_separately status from corresponding pipeline 73187bd - Updated PDF reporting text on IsoSeq with Mapping pipeline 4fa391c - Updated PDF reporting text on Read Segmentation and Single-Cell IsoSeq Pipeline 6162cd6 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v4.4.1 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Patch fixed PacBio's SMRT Link pb_segment_reads_and_isoseq WDL pipeline to support CSI index 5ea9ae4 - Added a new --kinnex option to format_barcode_csv script to help with running pb_segment_reads_and_isoseq pipeline by adding suffix to output file b32cad4 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v4.5.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Added support for asymmetric barcodes reads packaging for --pipeline demux_ccs f7e51e9 - Implemented a workaround to recreate fail_reads.consensusreadset.xml in the Data_Package (pb_formats) folder. Starting with SMRT Link v13.1.0.221970, fail_reads.consensusreadset.xml is no longer available in the raw sequenced reads location b304e2a |
| Type Of Technology | Webtool/Application |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v5.0.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - SMRT Link v25.1.0.257715 - Demultiplex Barcodes Support Release - Updated SMRT Link v13.1.0.221970 to SMRT Link v25.1.0.257715 #17 - Updated Revio run-qc report to support SMRT Link v25.1 1ef72a5 - Updated the recreate_raw_revio_output script to support SMRT Link v25.1 845c1ca - Added 6ma files to the final package 845c1ca - Ignored the *report.pdf from the raw reads from the final package 845c1ca - Updated configure docs 6d40535 - Updated paths and pipeline parameters and change 13.1.0.221970 to 25.1.0.257715 e1ae448 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) release v5.1.0 |
| Description | The EI PacBio Primary Analysis Pipeline (EIPACBIOPAP) is a Python3 and Snakemake-based workflow tailored for PacBio sequencing data analysis, including Sequel, Sequel IIe, and Revio SMRT cell data. The pipeline runs PacBio's SMRT Link software and consolidates the results for delivery to internal research faculty and external researchers and collaborators. EIPACBIOPAP optimally employs HPC resources and is adaptable to accommodate various PacBio platforms. Additionally, it produces high-quality LaTeX PDF reports summarising the results and seamlessly integrates with JIRA for output report dissemination. ** Main changes added to this release ** - Updated Snakemake to re-run run qc report on demultiplexed HiFi reads to generate consolidated plots 92cca6e - Updated script to get the consolidated plots generated from demultiplexed HiFi reads for reports 4267674 - Added a new feature to add a custom warning message to JIRA summarising the issue 5f3446d - Added checks and warnings to JIRA for cases when barcodes from the input Barcodes CSV file are missing in the demultiplexed output 0a5f700 - Added a limit (25 samples) to the number of samples on a page to avoid LaTex overflow 4267674 - Updated table header description under respective tables 2811326 - Fixed script to count only demultiplexed hifi_reads from both rules pb_demux_ccs_hifi_reads and pb_demux_ccs_fail_reads to check if we have the same number of barcoded reads in both hifi_reads and fail_reads stages post lima. It is required for the latest SMRT Link v25.1 ac22bd9 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | The EIPACBIOPAP pipeline plays a vital role in EI's sequencing facility, serving internal research faculty, external researchers, and collaborators. It assesses data, performs quality control, generates output BAM/FASTQ files, and produces detailed high-quality LaTeX PDF reports summarising the results. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eipacbiopap |
| Title | EI Repeat Pipeline (eirepeat) release v1.3.0 |
| Description | The EI Repeat (eirepeat) pipeline is a Python3 and Snakemake-based workflow intended for repeat identification in genomes. It is optimised for execution on High Performance Computing (HPC) clusters. Eirepeat serves as a wrapper around RepeatModeler and RepeatMasker, with an added option to run the RED (Repetitive Element Database) tool for repeat identification. Additionally, the pipeline supports filtering of identified repeats with close reference CDS FASTA and/or organelle genomes if provided. ** Main changes added to this release ** - Added script to convert RepeatMasker .out format to RepeatMasker .gff format when RepeatMasker fails to create it 4f6240b, 6a325b7 - Added new script to compute coverage of BED3 from GFF3 a484726 - Removed coverageBed to compute stats as it fails with wheat size genome with error 'ERROR: Received illegal bin number 37450 from getBin call. ERROR: Unable to add record to tree.' 80e7999 - Added missing --type match to add_directives_GFF3.py script to add directives 80e7999 - Added new option --exclude_hosts to 'eirepeat run' to exclude specific HPC hosts 74083ef - Added new PAP Jira email address 106277e - Added --keep-going option to enable run of independent jobs if a job fails db4d1a0 - Updated JIRA post to use JIRA Cloud b16219e - Updated README.md 0ed9f05, 300672b |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The eirepeat pipeline is essential for identifying repeats in the genome, serving as the initial step in genome annotation projects. It enhances the quality of genome annotation projects conducted internally for our research faculty, as well as for external researchers and collaborators. Additionally, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eirepeat |
| Title | EI Repeat Pipeline (eirepeat) release v1.4.0 |
| Description | The EI Repeat (eirepeat) pipeline is a Python3 and Snakemake-based workflow intended for repeat identification in genomes. It is optimised for execution on High Performance Computing (HPC) clusters. Eirepeat serves as a wrapper around RepeatModeler and RepeatMasker, with an added option to run the RED (Repetitive Element Database) tool for repeat identification. Additionally, the pipeline supports filtering of identified repeats with close reference CDS FASTA and/or organelle genomes if provided. ** Main changes added to this release ** - Added new pyproject.toml supporting python Poetry 91f394d - Added script 'merge_repeats' to merge repeats from input GFF3 fccb7e0 - Added seqkit option --only-id to extract only the fasta headers to prevent RepeatMasker failures 0ec3a24 - RepeatMasker does not create an output file '.masked' if it does not mask any bases. Create output file '.masked' for rule RepeatMasker_RepeatModeler if RepeatMasker completes successfully 26587d1 - Updated transposonPSI hpc_config.json to exclude a few nodes by default 30ea327 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The eirepeat pipeline is essential for identifying repeats in the genome, serving as the initial step in genome annotation projects. It enhances the quality of genome annotation projects conducted internally for our research faculty, as well as for external researchers and collaborators. Additionally, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eirepeat |
| Title | EI Repeat Pipeline (eirepeat) release v1.4.1 |
| Description | The EI Repeat (eirepeat) pipeline is a Python3 and Snakemake-based workflow intended for repeat identification in genomes. It is optimised for execution on High Performance Computing (HPC) clusters. Eirepeat serves as a wrapper around RepeatModeler and RepeatMasker, with an added option to run the RED (Repetitive Element Database) tool for repeat identification. Additionally, the pipeline supports filtering of identified repeats with close reference CDS FASTA and/or organelle genomes if provided. ** Main changes added to this release ** - Added seqkit option --only-id to extract only the fasta headers to prevent RepeatMasker failures 0ec3a24 - Update transposonpsi hpc_config.json to exclude a few nodes by default 30ea327 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The eirepeat pipeline is essential for identifying repeats in the genome, serving as the initial step in genome annotation projects. It enhances the quality of genome annotation projects conducted internally for our research faculty, as well as for external researchers and collaborators. Additionally, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eirepeat/releases/tag/v1.4.1 |
| Title | EI Repeat Pipeline (eirepeat) release v1.5.0 |
| Description | The EI Repeat (eirepeat) pipeline is a Python3 and Snakemake-based workflow intended for repeat identification in genomes. It is optimised for execution on High Performance Computing (HPC) clusters. Eirepeat serves as a wrapper around RepeatModeler and RepeatMasker, with an added option to run the RED (Repetitive Element Database) tool for repeat identification. Additionally, the pipeline supports filtering of identified repeats with close reference CDS FASTA and/or organelle genomes if provided. ** Main changes added to this release ** - Updated TransposonPSI to conda release version v1.0.0 edd0469 - Updated BEDTools to v2.31.1 0d1ef12 - Round up repeat summary stats for easy interpretation 8391f4f - Removed exclude node list for transposonpsi 766ea82 - Update README.md |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The eirepeat pipeline is essential for identifying repeats in the genome, serving as the initial step in genome annotation projects. It enhances the quality of genome annotation projects conducted internally for our research faculty, as well as for external researchers and collaborators. Additionally, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eirepeat/releases/tag/v1.5.0 |
| Title | EI Repeat Pipeline (eirepeat) release v1.5.1 |
| Description | Briefly describe the software or technical product. * The EI Repeat (eirepeat) pipeline is a Python3 and Snakemake-based workflow intended for repeat identification in genomes. It is optimised for execution on High Performance Computing (HPC) clusters. Eirepeat serves as a wrapper around RepeatModeler and RepeatMasker, with an added option to run the RED (Repetitive Element Database) tool for repeat identification. Additionally, the pipeline supports filtering of identified repeats with close reference CDS FASTA and/or organelle genomes if provided. ** Main changes added to this release ** - Possible fix for RepeatModeler error: FastaDB::getSubstr - Error index out of bounds! (SeqID=gi|310, offset=1945, length=71 actualSeqLen=1998) at /path/to/repeatmodeler/1.0.11/x86_64/bin/RepeatModeler line 2069. Command exited with non-zero status 25 6c14025 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The eirepeat pipeline is essential for identifying repeats in the genome, serving as the initial step in genome annotation projects. It enhances the quality of genome annotation projects conducted internally for our research faculty, as well as for external researchers and collaborators. Additionally, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/eirepeat/releases/tag/v1.5.1 |
| Title | Earlham Institute Mapping Pipeline (EIMAP) fix for v3.2.0 (fearensic_dev2) |
| Description | Fix a broken feature in the EIMAP pipeline which does coverage analysis and shows relationship between GC content and coverage. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2025 |
| Impact | EIMAP pipeline has being used to support EI's CellGen ISP activities and other single cell research projects. The pipeline has also been used to as a part of fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/ei-cuddly-happiness/tree/forensic_dev2 |
| Title | Earlham Institute Mapping Pipeline (EIMAP) release v3.1.1 |
| Description | The Earlham Institute Mapping Pipeline (EIMAP) is a Python3 and Snakemake-based workflow for Illumina sequencing QC, optimized for HPC resources. It provides QC metrics and interactive reports using MultiQC, processing output from the Earlham Institute Primary Analysis Pipeline (EIPAP) runs or external data. It is capable of handling DNA and RNA-seq samples and conducts various analyses like read subsampling, alignment, and assembly for RNA-seq. These analyses help determine sequence quality control such as like determine library strandedness, and detect genomic contamination. ** Main changes added to this release ** - Added new PAP Jira email address as part of the JIRA upgrade 0b36760 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Impact | The EIMAP pipeline is a critical component of EI's sequencing facility performing alignment-based analyses for sequencing quality control before providing data to both internal research faculty and external researchers and collaborators. This pipeline evaluates data, conducts quality control, and produces interactive HTML reports for user convenience. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/ei-cuddly-happiness |
| Title | Earlham Institute Mapping Pipeline (EIMAP) release v3.2.0 |
| Description | The Earlham Institute Mapping Pipeline (EIMAP) is a Python3 and Snakemake-based workflow for Illumina sequencing QC, optimized for HPC resources. It provides QC metrics and interactive reports using MultiQC, processing output from the Earlham Institute Primary Analysis Pipeline (EIPAP) runs or external data. It is capable of handling DNA and RNA-seq samples and conducts various analyses like read subsampling, alignment, and assembly for RNA-seq. These analyses help determine sequence quality control such as like determine library strandedness, and detect genomic contamination. ** Main changes added to this release ** - Added old library type 'ManualNEBNextUltraIIDirectionalRNASeqlibrarypolyAselection: RNA' for testing PSEQ-2416 82117d6 - Added new library type 'PacBioIsoSeqExpressTemplatePreparationSPK30nosizeselectionlibrary: RNA' 4d66de7 - Added new library types Illuminauniversaltailedampliconlibrary96wellplate, ONTUltraLongReadsLibrary, ONTLigationSequencingLibraryNativeBarcodingKit24V14, PacBioHiFiLibrarySMRTbellPrepKit30beadbasedsizeselection, PacBioHiFiLibrarySMRTbellPrepKit30BluePippinsizeselection10Kbinserts, PacBioHiFiLibrarySMRTbellPrepKit30ELFsizeselection1520Kbinserts 917ec81 - Added new library type DovetailOmniCLibrary as DNA pipeline 682fe0a - Added new library type LITE20LibraryPrep96wellplate and update SmartSeq2libraryprep96wellplatewithERCC 99b8be6 - Updated library_types.yaml 6e95c66 - Updated tgac-pap partition to ei-pap for kronos cluster f81dacd - Updated ReadMe 35a2be4 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIMAP pipeline is a critical component of EI's sequencing facility performing alignment-based analyses for sequencing quality control before providing data to both internal research faculty and external researchers and collaborators. This pipeline evaluates data, conducts quality control, and produces interactive HTML reports for user convenience. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/ei-cuddly-happiness |
| Title | Earlham Institute Primary Analysis Pipeline (EIPAP) release v3.1.1 |
| Description | The Earlham Institute Primary Analysis Pipeline (EIPAP) is a Python3 and Snakemake-based workflow designed for Illumina sequencing data analysis. It efficiently utilises HPC resources and is extensible to handle multiple Illumina platforms and libraries. EIPAP integrates data from JIRA and also posts output reports to JIRA, facilitating seamless user interaction. ** Main changes added to this release ** - Enabled params to pass through for bcl2fastq to fix #142 3f91f88 - Added changes to fix interop issues #139 #140 8186cf9 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Impact | The EIPAP is a critical component of EI's sequencing facility, providing data to both internal research faculty and external researchers and collaborators. This pipeline evaluates data, conducts quality control, generates output FASTQ files, and produces interactive HTML reports for user convenience. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eipap |
| Title | Earlham Institute Primary Analysis Pipeline (EIPAP) release v3.1.2 |
| Description | The Earlham Institute Primary Analysis Pipeline (EIPAP) is a Python3 and Snakemake-based workflow designed for Illumina sequencing data analysis. It efficiently utilises HPC resources and is extensible to handle multiple Illumina platforms and libraries. EIPAP integrates data from JIRA and also posts output reports to JIRA, facilitating seamless user interaction. ** Main changes added to this release ** - Fixed KeyError: 'parameters', add missing parameters to the config yaml files - demux.config.yaml and analysis.config.yaml f29461e |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Impact | The EIPAP is a critical component of EI's sequencing facility, providing data to both internal research faculty and external researchers and collaborators. This pipeline evaluates data, conducts quality control, generates output FASTQ files, and produces interactive HTML reports for user convenience. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eipap |
| Title | Earlham Institute Primary Analysis Pipeline (EIPAP) release v3.1.3 |
| Description | The Earlham Institute Primary Analysis Pipeline (EIPAP) is a Python3 and Snakemake-based workflow designed for Illumina sequencing data analysis. It efficiently utilises HPC resources and is extensible to handle multiple Illumina platforms and libraries. EIPAP integrates data from JIRA and also posts output reports to JIRA, facilitating seamless user interaction. ** Main changes added to this release ** - Removed loadPreCmd from bcl2fastq program_params c7354cb |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Impact | The EIPAP is a critical component of EI's sequencing facility, providing data to both internal research faculty and external researchers and collaborators. This pipeline evaluates data, conducts quality control, generates output FASTQ files, and produces interactive HTML reports for user convenience. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eipap |
| Title | Earlham Institute Primary Analysis Pipeline (EIPAP) release v3.1.4 |
| Description | The Earlham Institute Primary Analysis Pipeline (EIPAP) is a Python3 and Snakemake-based workflow designed for Illumina sequencing data analysis. It efficiently utilises HPC resources and is extensible to handle multiple Illumina platforms and libraries. EIPAP integrates data from JIRA and also posts output reports to JIRA, facilitating seamless user interaction. ** Main changes added to this release ** - Added a new PAP Jira email address as part of the JIRA upgrade 6151557 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Impact | The EIPAP is a critical component of EI's sequencing facility, providing data to both internal research faculty and external researchers and collaborators. This pipeline evaluates data, conducts quality control, generates output FASTQ files, and produces interactive HTML reports for user convenience. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eipap |
| Title | Earlham Institute Primary Analysis Pipeline (EIPAP) release v3.2.0 |
| Description | The Earlham Institute Primary Analysis Pipeline (EIPAP) is a Python3 and Snakemake-based workflow designed for Illumina sequencing data analysis. It efficiently utilises HPC resources and is extensible to handle multiple Illumina platforms and libraries. EIPAP integrates data from JIRA and also posts output reports to JIRA, facilitating seamless user interaction. ** Main changes added to this release ** - Added nextseq_1000 and removed nextseq to CLI e95fd5a - Changed default seqenv_config.yaml location 286a5da - Added a new platform and instrument NEXTSEQ_1000 082dee9 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Impact | The EIPAP is a critical component of EI's sequencing facility, providing data to both internal research faculty and external researchers and collaborators. This pipeline evaluates data, conducts quality control, generates output FASTQ files, and produces interactive HTML reports for user convenience. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eipap |
| Title | Earlham Institute Primary Analysis Pipeline (EIPAP) release v3.3.0 |
| Description | The Earlham Institute Primary Analysis Pipeline (EIPAP) is a Python3 and Snakemake-based workflow designed for Illumina sequencing data analysis. It efficiently utilises HPC resources and is extensible to handle multiple Illumina platforms and libraries. EIPAP integrates data from JIRA and also posts output reports to JIRA, facilitating seamless user interaction. ** Main changes added to this release ** - Added a new platform and instrument NOVASEQ_X_PLUS 778602a |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Impact | The EIPAP is a critical component of EI's sequencing facility, providing data to both internal research faculty and external researchers and collaborators. This pipeline evaluates data, conducts quality control, generates output FASTQ files, and produces interactive HTML reports for user convenience. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eipap |
| Title | Earlham Institute Primary Analysis Pipeline (EIPAP) release v3.3.1 |
| Description | The Earlham Institute Primary Analysis Pipeline (EIPAP) is a Python3 and Snakemake-based workflow designed for Illumina sequencing data analysis. It efficiently utilises HPC resources and is extensible to handle multiple Illumina platforms and libraries. EIPAP integrates data from JIRA and also posts output reports to JIRA, facilitating seamless user interaction. ** Main changes added to this release ** - Updated interop-1.1.6 to interop-1.2.4_CBG to fix interop issue #140 cc7f7f5 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Impact | The EIPAP is a critical component of EI's sequencing facility, providing data to both internal research faculty and external researchers and collaborators. This pipeline evaluates data, conducts quality control, generates output FASTQ files, and produces interactive HTML reports for user convenience. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eipap |
| Title | Earlham Institute Primary Analysis Pipeline (EIPAP) release v3.3.2 |
| Description | The Earlham Institute Primary Analysis Pipeline (EIPAP) is a Python3 and Snakemake-based workflow designed for Illumina sequencing data analysis. It efficiently utilises HPC resources and is extensible to handle multiple Illumina platforms and libraries. EIPAP integrates data from JIRA and also posts output reports to JIRA, facilitating seamless user interaction. ** Main changes added to this release ** - Added new rule copy_indexmetricsout_data to ensure the copy of IndexMetricsOut.bin to generate complete interop.index-summary ce09713 - Updated hpc_config.json to add new exclude hosts 82fadce |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPAP is a critical component of EI's sequencing facility, providing data to both internal research faculty and external researchers and collaborators. This pipeline evaluates data, conducts quality control, generates output FASTQ files, and produces interactive HTML reports for user convenience. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eipap |
| Title | Earlham Institute Primary Analysis Pipeline (EIPAP) release v4.0.0 |
| Description | The Earlham Institute Primary Analysis Pipeline (EIPAP) is a Python3 and Snakemake-based workflow designed for Illumina sequencing data analysis. It efficiently utilises HPC resources and is extensible to handle multiple Illumina platforms and libraries. EIPAP integrates data from JIRA and also posts output reports to JIRA, facilitating seamless user interaction. ** Main changes added to this release ** - Breaking Change - Kronos cluster - Changed default transfer copy command from 'cp' to 'rsync' f8cfa15 - Added new eitransfer load variable to eipap_config.yaml a97b516 - Updated hpc_config.json for eitransfer and kronos cluster 54dbf69, 2025b3e - Added hpc config and pap config to transfer script 2089e27 - Changed tgac-pap partition to ei-pap d7fe76a - Updated ReadMe 163266c |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPAP is a critical component of EI's sequencing facility, providing data to both internal research faculty and external researchers and collaborators. This pipeline evaluates data, conducts quality control, generates output FASTQ files, and produces interactive HTML reports for user convenience. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eipap |
| Title | Earlham Institute Primary Analysis Pipeline (EIPAP) release v4.1.0 |
| Description | The Earlham Institute Primary Analysis Pipeline (EIPAP) is a Python3 and Snakemake-based workflow designed for Illumina sequencing data analysis. It efficiently utilises HPC resources and is extensible to handle multiple Illumina platforms and libraries. EIPAP integrates data from JIRA and also posts output reports to JIRA, facilitating seamless user interaction. ** Main changes added to this release ** - Added custom sequential execution using resources to limit parallel 'rule bcl2fastq' jobs f0ca86a |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPAP is a critical component of EI's sequencing facility, providing data to both internal research faculty and external researchers and collaborators. This pipeline evaluates data, conducts quality control, generates output FASTQ files, and produces interactive HTML reports for user convenience. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eipap |
| Title | Earlham Institute Primary Analysis Pipeline (EIPAP) release v4.2.0 |
| Description | The Earlham Institute Primary Analysis Pipeline (EIPAP) is a Python3 and Snakemake-based workflow designed for Illumina sequencing data analysis. It efficiently utilises HPC resources and is extensible to handle multiple Illumina platforms and libraries. EIPAP integrates data from JIRA and also posts output reports to JIRA, facilitating seamless user interaction. ** Main changes added to this release ** - Added new option --sequential_bcl2fastq to control sequential bcl2fastq runs when required 2d688fa #150 - Updated README.md with --sequential_bcl2fastq option bc434b5 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The EIPAP is a critical component of EI's sequencing facility, providing data to both internal research faculty and external researchers and collaborators. This pipeline evaluates data, conducts quality control, generates output FASTQ files, and produces interactive HTML reports for user convenience. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eipap |
| Title | Earlham Institute Web Apollo Browser (eiwebapollo) release v4.0.0 |
| Description | The Earlham Institute Web Apollo Browser (eiwebapollo) suite is written in Python3 and enables the creation, formatting, and loading of files to EI's Web Apollo browser instance, utilizing Apollo - a collaborative, real-time, genome annotation web-based editor (https://genomearchitect.readthedocs.io/en/latest/). The suite provides functionalities for formatting output files generated by various software and includes scripts for generating browser-specific GFF3 files. It simplifies the creation of a new Apollo browser instance and loading files by maintaining a structured approach for all projects at EI. This suite plays a crucial role in visualizing models in the browser, thereby enhancing the quality of genome annotation projects. ** Main changes added to this release ** - Upgraded Apollo to v2.6.6 release - Renamed apollo to eiwebapollo 32a3e79 - Added new eiwebapollo to setup cfb7d19 - eiwebapollo setup implemented 705a51a - eiwebapollo load implemented 4ff58b0 - Added migrate_apollo script f8f0580 - Added --new_category to eiwebapollo load and change /ei/shared/ to /ei/services/webapollo/ 03a3eb7 - Use the original key when migrating old browser instance 1ecb22f - Skip track migration if file_format cannot be inferred 36db04c - Skip track migration if 'style' is not defined f90d0c8 - Skip track migration if 'category' is not defined c55d739 - Added new browsers to eicb group to share with team 4d9d4fb - Added version details 64233f2 - Added environment.yml requirements.txt a3af84c - Updated requirements 90ae940 - Updated setup.py with name apollo and python requirements 643946e - Added key, label and category information for skipped tracks 3846f5c - Refactored the codebase 7b3eb99 - Added new script to get protein coding models from GFF3 file based on biotype 2a4238f - Updated migrate_apollo help d864a34 - Updated setup help 988c0dd - Updated README.md 0ebc768,f55bc31 - Updated logging and refactor 9577804, e948ec5, 221634e |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The eiwebapollo suite plays a crucial role in visualizing models in the browser, thereby enhancing the quality of genome annotation projects we do internally for the research faculty and external researchers and collaborators. Additionally, it has been utilized as part of a fee-for-service offering. |
| URL | https://github.com/EI-CoreBioinformatics/eiwebapollo |
| Title | Mikado: a pipeline to determine and select the best RNA-Seq prediction | Release v2.3.5rc2 |
| Description | Mikado is a lightweight Python3 pipeline to identify the most useful or "best" set of transcripts from multiple transcript assemblies. Our approach leverages transcript assemblies generated by multiple methods to define expressed loci, assign a representative transcript and return a set of gene models that selects against transcripts that are chimeric, fragmented or with short or disrupted CDS. Loci are first defined based on overlap criteria and each transcript therein is scored based on up to 50 available metrics relating to ORF and cDNA size, relative position of the ORF within the transcript, UTR length and presence of multiple ORFs. Mikado can also utilize blast data to score transcripts based on proteins similarity and to identify and split chimeric transcripts. Optionally, junction confidence data as provided by Portcullis can be used to improve the assessment. The best-scoring transcripts are selected as the primary transcripts of their respective gene loci; additionally, Mikado can bring back other valid splice variants that are compatible with the primary isoform. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Mikado software plays a vital role in powering our REAT (https://github.com/EI-CoreBioinformatics/reat) and Minos (https://github.com/EI-CoreBioinformatics/minos) pipelines, contributing to diverse annotation projects at the Earlham Institute. The release of the Mikado Docker image on Docker Hub (https://hub.docker.com/r/gemygk/mikado) has facilitated its wider accessibility, evidenced by 141 pulls in just five months, demonstrating its value to the research community. |
| URL | https://github.com/EI-CoreBioinformatics/mikado |
| Title | Minos - a gene model consolidation pipeline for genome annotation projects |
| Description | Minos is a Python3/Snakemake - based pipeline that generates and utilises metrics derived from protein, transcript and expression data sets to consolidate gene models obtained from gene annotation workflows. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The tool has bee used to deliver annotation for 9 wheat accessions as part of the 10+ Wheat Genomes Project (http://www.10wheatgenomes.com/) and is being used to support a variety of Earlham Institute annotation projects and featured as part of Biohackathon Europe 2023 https://doi.org/10.37044/osf.io/fy49g |
| URL | http://www.10wheatgenomes.com/ |
| Title | Minos - a gene model consolidation pipeline for genome annotation projects | 2024 Updates |
| Description | Minos is a Python3/Snakemake pipeline designed to consolidate gene models from gene annotation workflows by generating and utilising metrics derived from protein, transcript, and expression datasets. ** Main changes added to this release ** - Reordered the lookup to look at CPC models next if Mikado models are absent in the metrics_info.txt file to get the full list of models 3d9d22f - Introduced a configurable chunk size parameter within minos_config.yaml for BLAST and DIAMOND jobs, effectively mitigating HPC overhead. (8fed890) - Corrected threshold parameters for BLAST and DIAMOND BLASTP filtering, improving the accuracy of sequence similarity assessments. (c5b7d1f) |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The Minos pipeline has been used to deliver diverse annotation projects at the Earlham Institute. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/minos |
| Title | REAT - Robust and Extendable eukaryotic Annotation Toolkit (2023 updates) |
| Description | REAT is a robust easy-to-use genome annotation toolkit for turning high-quality genome assemblies into usable and informative resources. REAT makes use of state-of-the-art annotation tools and is robust to varying quality and sources of molecular evidence. REAT provides an integrated environment that comprises both a set of workflows geared towards integrating multiple sources of evidence into a genome annotation, and an execution environment (Docker, Singularity) for these workflows. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | Being used to support EI's annotation projects including the DToL Protist project Components of the toolkit were developed to support the annotation of wheat accessions as part of the 10+ Wheat Genome Project. Assessed as part of Biohackathon Europe 2023 https://doi.org/10.37044/osf.io/fy49g |
| Title | REAT - Robust and Extendable eukaryotic Annotation Toolkit | 2024 Updates |
| Description | REAT is a robust easy-to-use genome annotation toolkit for turning high-quality genome assemblies into usable and informative resources. REAT makes use of state-of-the-art annotation tools and is robust to varying quality and sources of molecular evidence. REAT provides an integrated environment that comprises both a set of workflows geared towards integrating multiple sources of evidence into a genome annotation, and an execution environment (Docker, Singularity) for these workflows. ** Main changes added to this release ** - Breaking update - REAT Homology Miniprot Integration - Harmonise conda dependencies and installation 7063181 - Updated REAT singularity definition file and updated software to make them compatible with rest of the tools 3494464 - Added new generic script create_mgc_groups_from_gff.py to create groups.txt file for multi genome compare from the alignments GFF file 1588ffe - Added new script to reformat miniprot GFF from mRNA->CDS to gene->mRNA>[exon|CDS] OR match->match_part format - miniprot2GFF3.py 24a3000 - Added new script to create alignment summary from multi_genome_compare --detailed tab output file - create_alignment_summary.py 7e69707 - Fixed missing '--source' to the spaln2gff output gff3 697aa21 - Changed default coverage and identity to '0' in spaln2gff script 5883703 - Round float to int before binning - create_alignment_summary.py 3857669 - Added checks to --spaln_extra_parameters to have -Q and -A parameters specified and not to include options -t, -K, -O, -Q, -M, -T, -d, -o, -yL ee874ca - Added spaln and miniprot specific options for running REAT homology WDL pipeline ee874ca - Renamed output 'all_avgF1.bin.txt' to 'Junction_precision_binning.tsv' ee874ca - Reorganised REAT homology outputs folder ee874ca - Added miniprot support to REAT Homology pipeline 3947259 - Updated splan command to incorporate new pass through parameters 3947259 - Added a common 'task_attr' to manage HPC resource for additional workflow tasks 3947259 - Refactored task 'ScoreSummary' by incorporating create_alignment_summary.py script 3947259 - Changed rt_struct.wdl to common/rt_struct.wdl 3947259 - Changed task 'PrepareAnnotations' min_exon_len to 10 from 203947259 - Changed task 'PrepareAlignmentsSpaln' min_filter_exon_len to 10 from 20 3947259 - Removed recursion_level option from splan alignments tasks 3947259 - Updated list of software_available to the latest versions used for installation 5e1850b - Added new option --spaln_extra_parameters to pass on extra parameters for SPALN alignment, where user must include the -Q and -A parameters 5e1850b - Fixed incorrect parameter from --alignment_min_exon_len to --alignment_max_intron_length 5e1850b - Added new minimum intron length, alignment parameter (spaln) --alignment_min_intron_length 5e1850b - remove SPALN's Q value parameter --alignment_recursion_level, indicating the level of recursion for the Hirschberg algorithm, which is now part of the --spaln_extra_parameters 5e1850b - Changed --filter_min_exon default value from 20 to 10 5e1850b - Updated help docs to make it more clearer 5e1850b - Updated help docs - xspecies_cleanup 64a5d9e - Updated help docs - filter_GFF3_terminals.py e2721f7 - Added additional WDL's to package_data - setup.py 059d1b7 |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The REAT pipeline has been used to deliver diverse annotation projects at the Earlham Institute. Furthermore, the pipeline has also been used as part of a fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/reat |
| Title | User Documentation | COPO Project |
| Description | The Collaborative OPen Omics (COPO) documentation was created using the Sphinx reStructuredText (reST) markup language and hosted on Read the Docs. Read the Docs is a popular platform for hosting documentation, and it is used by many open-source projects whereas Sphinx is a powerful tool that makes it easy to create professional documentation. This version of the COPO documentation replaces the previous version which was last updated in 2021. In addition, the Help section of the COPO web application was omitted and included in this version of the COPO documentation. The latest version of the COPO documentation comprises the following sections: - Getting Started This section provides an overview of the COPO web application. It includes information on how to create an account, log in, and navigate to the COPO web application. - COPO Profile This describes the types of work profiles that can be created in COPO as well as how to create and manage them. - COPO Data Submission This describes the various ways by which metadata can be uploaded and submitted to COPO. - COPO Data Updates This describes how submitted metadata can be updated in COPO and what metadata cannot be updated - COPO Data Discovery & Retrieval - This describes how to search for metadata in COPO and how to retrieve metadata from COPO - Advanced This describes how to set up the COPO project locally with Docker and with PyCharm or Visual Code Code (VSCode) - Polices This describes the policies that govern the use of COPO - Help This section describes the glossary of terms used in COPO web application, how to contact the COPO team regarding issues or enquiries and frequently asked questions (FAQs) |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The new version of the COPO documentation provides users with a comprehensive and updated guide to using the COPO web application and the COPO API. It comprises the following sections: - Getting Started - COPO Profile - COPO Data Submission - COPO Data Updates - COPO Data Discovery & Retrieval - Advanced - Polices - Help |
| URL | http://copo-docs.readthedocs.io |
| Title | singlecellQC - Smart-Seq2 quality control pipeline (2023 updates) |
| Description | singlecellQC is a Smart-Seq2 quantification and quality control pipeline, developed for single-cell service at the Earlham Institute. Starting with the FASTQ files generated from the SmartSeq2 experiment and a sample sheet containing the appropriate metadata, transcript level counts are generated, merged and used to produce QC metrics. A QC report document is generated for each of the plates, and the whole experiment. The pipeline does not require internet connection, but some required files have to be precomputed. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | Being used to support EI's CellGen ISP activities and other single cell research projects. The pipeline has also been used to as a part of fee-for-service. |
| URL | https://github.com/EI-CoreBioinformatics/singlecellQC/tree/main_dev_branch |
| Description | Advanced Single-Cell RNAseq Data Analysis (6-9 November 2023) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This course provided a deep dive into single-cell genomics, for researchers who are in the early stages of planning a single-cell project. The course consisted of a mixture of conceptual and methodological lectures and hands-on bioinformatics sessions, including best practice and tips as learned first-hand by Earlham Institute's faculty. Participants gained first-hand experience by learning how to assess data quality with the guidance of the faculty, troubleshoot small problems, and review the results. Hands-on sessions used data generated using both Smartseq2 and 10X protocols. This in-person course had 19 attendees, with 52% from the UK, but also participants from, Belgium, Chile, Germany, Hong Kong, Hungary, India, Japan, and Spain. 43% were PhD Students, and 19% were Post Docs. 100% said the Overall Quality was very good/excellent. 100% said the Trainers were Very Good or Excellent. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/advanced-single-cell-rnaseq-data-analysis-2023 |
| Description | Are you a research technician? |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | We wrote an article about the diversity of technical roles within the Earlham Institute, and how many of them could benefit from the Technician Commitment but might not naturally identify with this title. The piece raised a question that the community has often debated and it generated a lot of engagement and comments on social media, with the official Technician Commitment accounts sharing the piece on their own channels. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/articles/are-you-research-technician |
| Description | Brabram Institute My Life in Science Seminar Series (KG) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Organised by the Babraham Institute, the My Life in Science seminar series aims to increase the exposure of PhD students and postdocs to excellent role models and the realities of a career in research. As core facility lead and first male speaker in the series, Dr Karim Gharbi talked about his journey through science, reflecting on the people, decisions, and opportunities that have influenced his career as a technically-minded biologist. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.babraham.ac.uk/work-and-study/e4s/events-and-activities |
| Description | Case Study: Applying automation expertise to support new technology development |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | We worked with the Technical Genomics and Business Development and Impact Groups, to write up a case study of EI's collaboration with SPT Labtech on the development of firefly. The case study showcases the impact of a BBSRC Flexible Talent Mobility Award (FTMA) award to the Earlham Institute, that saw Tom Brabbs, Senior Scientist and Jim Lipscombe, Senior Research Assistant, be placed at SPT to develop, test, and adapt a DNA sequencing workflow based on the LITE protocol. The piece was written in collaboration with the team at SPT Labtech. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.earlham.ac.uk/case-study-applying-automation-expertise-support-new-technology-developmen... |
| Description | Covering vast regions with one long read |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | To support the Norwich Nanopore Day activity, we wrote an article with Dr Conrad Nieduszynski and Dr Karim Gharbi about the expertise and capabilities of long-read nanopore sequencing at the Earlham Institute. This acted as a promotional tool for the event, but also linked with our key communications activities, including event promotion for our Nanopore training events, our Delivering Sustainable Wheat article, and the Institute's ISPs and NBRIs. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/articles/covering-vast-regions-one-long-read |
| Description | Devastating crop pathogens can be found by sequencing the air |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | News release based on the publication demonstrating the accuracy of AirSeq. This followed earlier press activity about sequencing the air in Norfolk and was therefore popular online. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/news/devastating-crop-pathogens-can-be-found-sequencing-air |
| Description | EI Innovate FTMA SPT Labtech Project Flash Talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Gave a flash talk summarising 2022 FTMA project carried out with SPT Labtech (development of a minaturised DNA Prep method for SPT's new Firefly robot). The talk highlighted what we did during the project and what both parties got out of it, i.e. the importance of KEC with industry. |
| Year(s) Of Engagement Activity | 2023 |
| Description | EI Innovate annual stakeholder engagement event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | EI Innovate is an annual engagement event that provides insight into the Earlham Institute's research, exploring opportunities for innovation and collaboration. Specialising in agri-food, biotech, med-tech and public health, we have a wealth of experience collaborating with others to develop potential solutions to urgent industrial and societal challenges. EI Innovate events foster exciting and valuable conversations between academia and industry. An example of an exciting collaboration that resulted from a previous EI Innovate is the Hybrid Wheat Initiative, which connects 25 breeding companies and research institutes worldwide, to resolve the critical challenge of hybrid wheat. In 2023, we showcased our two new strategic programmes of research - Cellular Genomics and Decoding Biodiversity - and two National Bioscience Research Infrastructures (NBRIs) - Transformative Genomics and the Earlham Biofoundry. The programme included talks about Earlham expertise and capabilities, examples of collaborations, panel discussions, Innovation Showcase, exhibition, tours of the two National Bioscience Research Infrastructures (NBRIs) - Transformative Genomics and the Earlham Biofoundry, and networking. |
| Year(s) Of Engagement Activity | 2019,2020,2021,2022,2023 |
| URL | https://www.earlham.ac.uk/events/ei-innovate-2023 |
| Description | Excellent science? It's in the technical detail |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article on the Institute's status as a Technician Commitment signatory, designed to inform and influence the opinions of internal and external audiences. We saw a positive response internally as people felt recognised and saw visibility given to colleagues who may have been overlooked for their past contributions. The piece also invited ideas for follow-up content on the different kinds of technical roles and their contributions. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/articles/excellent-science-its-technical-detail |
| Description | Festival of Genomics 2024 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The Earlham Institute exhibited at the Festival of Genomics and Biodata in London - an event attended by around 5,000 people. Complemented by talks and panel discussions delivered by our researchers, our stand provided an opportunity to showcase our science, technology platforms, and opportunities for engagement. EI delegates collectively had more than 100 conversations about the Institute, ranging from interest in jobs or PhDs to requests for scientific services. The true impact of attendance will be felt over the long-term, with a few potential collaboration opportunities being explored. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://festivalofgenomics.com/london/en/page/home |
| Description | Festival of Genomics 2025 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | We exhibited at the Festival of Genomics & Biodata in London, taking a stand to raise our profile, strategically flag particular services and research areas, and to connect with other attendees for follow-up opportunities. We were seen by the majority of delegates, spoke to more than 100, and have follow-up actions with around 40-50 of them. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://festivalofgenomics.com/london/en/page/2025-homepage |
| Description | Genome Annotation Workshop (May 2024) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | In this three-day, virtual course participants gained an overview of Next Generation Sequencing technologies relevant to genome annotation, gaining the benefits of each platform, including the use of a number of tools developed at EI to support high-quality annotation (Mikado and Portcullis, PMIDs 30052957 and 30418570 respectively). Through a programme of talks, demonstrations and hands-on sessions all lead by EI faculty, topic covered were: • Understanding what to look for in a sample that will pass quality control and that will likely succeed in producing viable sequencing data, including how to assess the quality of RNA-Seq data. • Learn about reference guided transcriptome assembly and steps for processing short and long read data. • Learn about alternative approaches for annotating protein coding genes in eukaryotic species utilizing transcriptome and homology data, via projection and evidence guided gene prediction. Discuss the challenges of annotation in different contexts. • Hands on experience of annotation tools including tools and pipelines developed at the Earlham Institute. You will build gene models, explore the use of combiners/choosers for integrating alternative gene predictions (EVM / MINOS) and assess the accuracy of different annotation tools. The course had 25 attendees, with 88% from academia. International attendees made up 40% of the cohort, attending virtually from Australia, Austria, Belgium, France, Germany, Netherlands, Philippines, Taiwan and United States. 100% of attendees that provided feedback would recommend the course, and rated the Trainers, Overall Quality of the event and Training Materials as Excellent or Very Good. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/genome-annotation-workshop-2024 |
| Description | How to use spatial transcriptomics to view single plant cells in situ |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | We worked with Ashleigh Lister in the Macaulay Group to publish a technical-led blog highlighting the workflow used for spatial transcriptomics in plant tissue. The aim of the blog was to profile Ashleigh's, and the Institute's, leading expertise in applying this technology to non-model organisms, and to further promote the capability as part of the Single-Cell team and NBRI in Transformative Genomics. The blog was incredibly well engaged with on social and on the website and continues to be one of the most popular blogs on our website. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/articles/how-use-spatial-transcriptomics-view-single-plant-cells-situ |
| Description | Image Processing with Python (11-12 June 2024) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | This two-day, in-person workshop gave researchers a thorough grounding in using Python to process and analyse image data. It was aimed at researchers who have a working knowledge of Python and who expect to be producing volumes of image data that would benefit from some automated analysis. Participants learnt the fundamentals of image processing using the skimage library to analyse many different properties of an image, primarily focused on morphometrics, but which are widely applicable to a range of image analysis problems. Starting with how images are represented in digital format, the pros and cons of different image file formats, metadata and how images are stored in arrays, the course moved through various lessons to explore image data, implementing bitwise operations, masks, filtering and thresholding to optimise your analysis. The workshop culminated in a hands-on exercise that provided participants with the opportunity to combine the approaches learned throughout all the previous lessons. 56% of attendees were from Norwich Research Park, with the others with the UK. All attendees who provided feedback rated the Trainers and the Overall Quality as very good/excellent, 100% would also recommend the course to others. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/image-processing-python-2024 |
| Description | Industry Seminar Babraham Institute 10/10/2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | The day was made up of a networking brunch for BI visitors & a selection of EI colleagues. This was followed with a discussion around best practice for working with industry. This was followed with 2 workshops on the following topics, Budget, pricing and project management, Building skillset for working with industry among technical staff, Inter-institute projects and services (blue sky), Training and staff exchanges & then a whole group discussion to summarize the workshops. There was a networking lunch for students with BI then delivered a 60 minute seminar which was open to all colleagues at EI. The day lead to building new relationships & looking at good practices and Knowledge Exchange. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Innovate UK Edge Event "Meet the Stakeholder" (08/09/2023) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | BN presented at an Innovate UK EDGE, Meet the Stakeholder meeting on 8th September, where how to work with the ISPs and NBRIs was presented to the EDGE team, along with EI's new position as a registered RTO/ Catapult Growth Grant supplier. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Introduction to Single-Cell RNAseq (18-20 Sep) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | This course provided an introduction to Single Cell Genomics. It covered several aspects of single-cell workflows from experimental design to laboratory hands-on including cell sorting and processing for production of quality samples for sequencing, generation of sequencing data and introduced tools and metrics for assessing the data quality. Laboratory practicals involved cell sorting using FACS AriaFusion, including considerations for different cell types, preparation of samples for Smart-seq, library construction, QC and pooling, loading of the 10X instrument. Delegates had the opportunity to review sequencing reports to determine data quality, interpret library and pre-processing QC, understand the principles of producing matrices, and identify any filtering required. The course consisted of a mixture of conceptual lectures, methodological lectures, and hands-on sessions in the laboratory. 58% of the participants were either at PhD or PostDoc level. 42% were from the Norwich Research Park, the other participants came from across the UK. The feedback for the Trainers, and Overall Course Quality both received 100% Excellent feedback. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/introduction-single-cell-rnaseq-2023 |
| Description | Key tilapia genome offers boost to global food security |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | News story to highlight a new publication from EI researchers on reference genome for a key aquaculture species, designed to reach breeders, industry, and academics working in this space. Positive trade media coverage, as well as promotion from project collaborators, helped this news to reach a wide audience and enhance EI's reputation. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/key-tilapia-genome-offers-boost-global-food-security |
| Description | LITE2 takes affordable genome sequencing to a new level |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | We published an article on the LITE2 protocol to celebrate the innovation behind it and encourage people to start using it as a service. The piece highlights the people and technical innovation behind some of the things we offer through the NBRI, and will be used as a long term piece of content to market this as a service. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.earlham.ac.uk/articles/lite2-takes-affordable-genome-sequencing-new-level |
| Description | Low-protein diets offer protective effect during bacterial infection |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A news release based on a publication by Edyta Wojtowicz in partnership with the Quadram Institute, highlighting research looking into protein in diet and the immune system response. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/news/low-protein-diets-offer-protective-effect-during-bacterial-infection |
| Description | Mapping cell diversity with LRS and Single-Cell |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | We published an article on the Macaulay Group's research combining single-cell and long-read sequencing technologies. This highlighted our innovation and long involvement in the maturation of these technologies, showcasing our expertise with them. It supports both the work that is being delivered through the Cellular Genomics ISP as well as the Transformative Genomics NBRI. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.earlham.ac.uk/articles/mapping-cell-diversity-long-read-sequencing-and-single-cell-genom... |
| Description | Minaturised DNA Prep GenomeWeb Webinar (SPT Labtech FTMA Project) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Gave a webinar on the FTMA project we did with SPT Labtech. For this project we developed a method to carry out miniaturised DNA Prep library preparation on SPT's new Firefly robot. Webinar went over the method and the results of the validaiton experiments showing its performance was comparable to the full volume method. Talk was well received and will led to a KEC case study with SPT Labtech. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://event.on24.com/wcc/r/3775808/501E66A8D4A59C6047567B38D809E833?skipwc=1&email=Thomas.Brabbs%4... |
| Description | NBI Accessible Science Event 2023 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Schools |
| Results and Impact | A "flash talk" explaining how I arrived at my current career position despite a limited education. The audience consisted of school and university students, researchers, technicians and others, both in person and online. Some audience members joined online from the USA and India as well as from local schools. The event was in part designed to highligh the important role that technical staff play in research; I described my role as an automation specialist within my group. |
| Year(s) Of Engagement Activity | 2023 |
| Description | New sequenced genome sheds light on weed resistance |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | We collaborated with Rothamsted Research to promote the publication of a reference genome that would be of enormous value to crop breeders and those working in agriculture. The project relates to an ERGA pilot and wider work on generating reference quality genomes to support new science. The piece received trade coverage and generated positive engagement on social media. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.earlham.ac.uk/news/new-sequenced-genome-sheds-light-weed-resistance |
| Description | Norwich Single-Cell Symposium (26-27 June 2024) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This two-day, in-person event brought together researchers who are curious about applying single-cell technologies with those who are experts working at the forefront of the field and across a wide range of species. The symposium covered single-cell genomics technologies and their application in microbial, plant, animal and human health and disease. Offering a forum for researchers working on similar challenges in diverse systems to discuss the latest developments in single-cell genomics, while networking with other researchers with the intention of catalysing future development and application of single-cell genomics across the UK. The event featured talks from keynotes, invited speakers and selected abstracts, and we were keen to include as broad a range of single-cell applications as possible. Topics covered included: Topics covered included: • Single-cell genomics in plant and microbial research • Single-cell genomics in health, disease and development • Single-cell informatics • Single-cell technology development. Networking was facilitated within an evening reception and elongated breaks between talk sessions. The symposium had 90 attendees, including 2 keynote speakers, 6 invited speakers and 9 speakers selected from abstract submission. Five attendees presented posters through abstract submission. Feedback summary: 100% of the feedback we received rated the symposium as Very Good/Excellent, with 97% of saying they would like to attend a future occurrence of the event. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/norwich-single-cell-symposium-2024 |
| Description | Norwich Single-Cell Symposium 2023 (3 May 2023) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This event brought together researchers who are curious about applying single-cell technologies with those who are experts working at the forefront of the field and across a wide range of species. The symposium covered single-cell genomics technologies and their application in microbial, plant, animal and human health and disease. Offering a forum for researchers working on similar challenges in diverse systems to discuss the latest developments in single-cell genomics, while networking with other researchers with the intention of catalysing future development and application of single-cell genomics across the UK. The event featured talks from keynotes, invited speakers and selected abstracts, and we were keen to include as broad a range of single-cell applications as possible. Topics covered included: • Single-cell genomics in plant and microbial research • Single-cell genomics in health, disease and development • Single-cell informatics • Single-cell technology development The symposium had 90 attendees, including two keynotes and 10 speakers. 90% of the feedback we received rated the symposium as Very Good/Excellent. 90% also describe the event as 'providing an update on breakthroughs and emerging technologies in the single cell field'. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/norwich-single-cell-symposium-2023 |
| Description | NovaSeq X Plus platform at EI 2023 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The Earlham Institute issued a press release announcing that it was the first UK site - and among the first in Europe - to receive the latest platform from Illumina - the NovaSeq X Plus. Our story and related social media campaign had more than 17,000 impressions and over 550 engagements, raising both the profile of both EI and the technology platforms we can offer the community. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/earlham-institute-first-uk-site-receive-illumina-novaseq-x-plus |
| Description | Outreach talk (Langwith Bassett Garden Club) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | An evening presentation and open discussion with a community hobby group (gardening club) about single-cell biology, and the work of our group and Institute. This was a 45-min presentation followed by Q&A and open discussion around the role of single-cell biology techniques in health and disease, envionmental protection, food security and gave a diverse and demographically wide-ranging audience an opportunity to find out more about what science we are doing and how this can help them, and society in general. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Pan-European project generates genomes showcasing continent's rich biodiversity |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A news story supporting the European Reference Genome Atlas Pilot Project. The story showcases the success of the pilot project and highlights the wide-ranging involvement from the Earlham Institute including the Technical Genomics, Haerty, Anthony Hall, and Neil Hall Groups, as well as the role of the National Bioscience Research Infrastructure in Transformative Genomics. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/news/pan-european-project-generates-genomes-showcasing-continents-rich-bio... |
| Description | Presentation - Festival of Genomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | ~100 attendees at the Festival of Genomics were present for my talk on Single-cell long read sequencing |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation at the Innovation Showcase during EI Innovate 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | As part of the EI Innovate event in 2023, BDI team featured winners of the internal KEC Awards as part of the Innovation Showcase. JC, TB, JdV, WH, AH, JL presented their projects showcasing their KEC work - developing a spinout, a substantial collaboration, or a knowledge exchange activity with industry. EI Innovate is an annual engagement event that provides insight into the Earlham Institute's research, exploring opportunities for innovation and collaboration. Specialising in agri-food, biotech, med-tech and public health, we have a wealth of experience collaborating with others to develop potential solutions to urgent industrial and societal challenges. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/ei-innovate-2023 |
| Description | Single Cell RNAseq Bioinformatics Course (11-14 November 2024) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This in-person course provided a deep dive into single-cell genomics, for researchers who are in the early stages of planning a single-cell project. The course consisted of a mixture of conceptual and methodological lectures and hands-on bioinformatics sessions, including best practice and tips as learned first-hand by Earlham Institute's faculty. Participants gained first-hand experience by learning how to assess data quality with the guidance of the faculty, troubleshoot small problems, and review the results. Hands-on sessions used data generated using both Smartseq2 and 10X protocols, from both short- and long-read platforms. Registration for the course was offered on an open application basis with selection, with 23 applications resulting in 16 attendees. Demographics of attendees, 50% were from the UK, with participants also from France, Hungary, India, Iran, Spain and Turkey. The cohort was made up of 31% PhD students and 31% Post Docs, with the remainder 'Other', post-graduate students, and professors/PIs. 87.5% were based in academia, and 12.5% were from industry. Of the feedback received, 91% rated the trainers as Excellent and would recommend the course, and gave an overall quality rating of Very Good or Excellent. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/single-cell-rnaseq-bioinformatics-2024 |
| Description | Single-Cell RNAseq Laboratory (30 September - 03 October 2024) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This in-person, full-time, four-day course provided an introduction to Single Cell Genomics. It covered several aspects of single-cell workflows from experimental design to laboratory hands-on including cell sorting and processing for production of quality samples for sequencing, generation of sequencing data and introduced tools and metrics for assessing the data quality. Laboratory practical sessions involved cell sorting using FACS AriaFusion, including considerations for different cell types, preparation of samples for Smart-seq, library construction, QC and pooling, loading of the 10X instrument. Delegates had the opportunity to review sequencing reports to determine data quality, interpret library and pre-processing QC, understand the principles of producing matrices, and identify any filtering required. The course consisted of a mixture of conceptual lectures, methodological lectures, and hands-on sessions in the laboratory. All theory lectures and hands-on sessions included best practices and tips as learned first-hand by EI's own faculty. The course had 11 attendee, all from outside of the Norwich Research Park (one international, 10 based in the UK).The feedback for the Trainers, Overall Course Quality, and Overall Event Organisation all received 100% Excellent or Very Good rating for feedback received. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/single-cell-rnaseq-laboratory-2024 |
| Description | Single-cell show and tell |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | We organized the single-cell show and tell to showcase our equipment in the single-cell laboratories, talk about our workflows and provide some hands on lab experience to our colleagues within EI. We had 38 participants with different scientific and non-scientific backgrounds. The feedback was very positive, and most people would like to see other groups organize similar events. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Source of tilapia diversity now a threat to survival |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | News release to promote a publication from the Haerty Group on the impact of cross-breeding to tilapia diversity. The news story also highlighted the use of the Technical Genomics LITE protocol. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/news/source-tilapia-diversity-now-threat-survival |
| Description | Spatial Transcriptomics in Plants Workshop May 2024 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | tba |
| Year(s) Of Engagement Activity | 2024 |
| Description | Speed-networking (Sir Isaac Newton Sixth Form) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | A full day of rotation speed-networking where sixth form students are given the opportunity to engage with industry specialists across a range of informatic related careers. My role here was showcasing the role of a bioinformatician and the work of the institute. This was attended by all students at the sixth form college who are undertaking IT qualifications and thinking about university and career options. |
| Year(s) Of Engagement Activity | 2022,2023 |
| Description | Targeting global food insecurity with sustainable wheat |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | An article detailing the Earlham Institute's work contributing to the cross-institute Delivering Sustainable Wheat programme. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/articles/targeting-global-food-insecurity-sustainable-wheat |
| Description | Tecan NGS User Group Meeting LITE 2.0 Talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Invited to give a talk at the user group meeting on our new LITE 2.0 pipeline for low cost and input DNA sequencing. The talk changed people's view on the importance of method miniaturisation in genomics, particularly in Tecan. Talk has also led to potential new projects for the group. |
| Year(s) Of Engagement Activity | 2023 |
| Description | The end of genes: routine test reveals unique divergence in genetic code |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | News release: scientists testing a new method of sequencing single cells have unexpectedly changed our understanding of the rules of genetics. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/end-genes-routine-test-reveals-unique-divergence-genetic-code |
| Description | UEA Pharmacology Student Visit (27 January 2025) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | Twelve students, plus a staff member, from the University of East Anglia, attended Earlham Institute for an afternoon. They participated in lab tours of Genomics Pipelines, Single-cell Labs, and the Biofoundry. They then heard talks from researchers (talk titles below), and had an informal discussion with current PhD students at EI. Overview: What it means to do a PhD, DNA replication singled out Characterisation of alternative splicing regulation in the brain, Mining Meadows: Exploring the biosynthesis of bioactive compounds in medicinal plants |
| Year(s) Of Engagement Activity | 2025 |
| Description | UEA Pharmacology Student Visit - 12 Feb 2024 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | 13 students, plus a staff member, from the University of East Anglia, attended Earlham Institute for an afternoon. They participated in lab tours of Genomics Pipelines, Single-cell Labs, and the Biofoundry. They then heard talks from researchers (talk titles below), and had an informal discussion with current PhD students at EI. Overview: What it means to do a PhD DNA replication singled out Characterisation of alternative splicing regulation in the brain Clonal and molecular studies of haematopoiesis Mining Meadows: Exploring the biosynthesis of bioactive compounds in medicinal plants |
| Year(s) Of Engagement Activity | 2024 |
| Description | USA FDA - presentation by Silvia Ogbeide |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | PhD Student Silvia Ogbeide gave an invited talk on Single-cell multiomics to the US FDA omics workshop in February 2023 |
| Year(s) Of Engagement Activity | 2023 |
| Description | Using new technology to explore the tiniest of worlds |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | We wrote an article about the work of a PhD student in applying the latest technologies to explore microbiomes, which is connected to (though not funded by) our Cellular Genomics ISP. The piece highlighted our expertise and celebrated the work of a student, as well as the technology-driven science we are innovating with. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/articles/using-new-technology-explore-tiniest-worlds |
| Description | Visit from NNUH clinicians to the Earlham Institute on 19 June 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | BDI team and IM of the Earlham Institute organised the visit from NNUH clinicians to the Earlham Institute. We held a workshop for researchers and clinicians to discuss their interests in developing potential collaborative projects that would utilise earlham expertise and capabilities and NNUH access to patients and patient data, and to the Norwich Biorepository. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Visit of two Campden-BRI student competition winners (08 November 2024) |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | We provided a short visitors programme with tours of lab and computing infrastructure facilities and discussion meetings with faculty members as part of a UK tour for two student winners of the Graduate Research Video Competition in association with the US Institute of Food Technologies, supported by Campden BRI |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.campdenbri.co.uk/blogs/iftsa-winners-23-24.php |