About us
Learn how GA4GH helps expand responsible genomic data use to benefit human health.
Large-Scale Genomics (LSG) Work Stream
Develops products to describe, compress, store, encrypt, and transfer genomic data in a scalable way.
Genomic sequencing generates data at an increasingly large scale. As public and national health systems continue to adopt genomic testing and more private companies launch genomic projects, the vast quantity of raw sequencing data will only balloon further. The Large-Scale Genomics (LSG) Work Stream produces robust, standardised ways to describe, store, and access this vital genomic information.
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Image summary: The LSG Work Stream develops efficient formats to store, access, and analyse sequencing reads, genetic variation, and gene expression information.
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Technical description
Produces standardised file formats and remote access protocols for storing, compressing, encrypting, querying, and sharing genomic data at scale.
TOOLS & PLATFORMS
Products
Browser Extensible Data (BED)
Stores information on the location of genomic features
CRAM
Uses data compression strategies to efficiently store genomic data
Genetic Data Encryption (Crypt4GH)
Provides an encrypted file format to keep data secure throughout its lifetime while allowing random access
Genetic Variation Formats (VCF)
Provides a text file format for storing genetic variation data
htsget
Allows users to download read and variation data for subsections of the genome
refget
Employs a computer algorithm to unambiguously identify reference sequences for genomic analysis
RNAget
Provides a common set of communication channels to efficiently retrieve RNA data of interest
SAM/BAM
Provides a format for storing next-generation sequencing read data
Sequence Annotation (SA)
Aims to develop a flexible, common model for describing genomic features
Variant Benchmarking Tools
Offers methods for robustly checking variant call accuracy
WGS Quality Control Standards
Describes a set of quality control metrics and their detailed definitions to facilitate exchange of results across initiatives
Publications
Community Resources
Dive deeper into our Work Stream! LSG produces standardised methods for storing, accessing, and analysing genomic data (reads, variants, and expression data) on a large scale. For remote queries, the Work Stream also develops standards for file-based, API-based, cloud-based, and distributed access.
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Date
Title
Info
29 Feb 2024
Please review the document by Wednesday, 30 March 2024.
15 Feb 2023
Please review and provide your feedback for CRAM v3.1 and refget v2.0 by 14 March 2023.
27 Oct 2022
Please submit feedback by Thursday, 1 December 2022, at 17:00 UTC.
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Title
Info
Repeat
Day
Time
Duration
This group meets to discuss all GA4GH File Formats maintained by the Large-Scale Genomics Work Stream: SAM/BAM/CRAM and VCF/BCF.
Every Two Months
Tuesday
00:00 UTC
1 Hour
This group meets to discuss all GA4GH File Formats maintained by the Large-Scale Genomics Work Stream: SAM/BAM/CRAM and VCF/BCF.
Every Two Months
Tuesday
20:00 UTC
1 Hour
This group meets to discuss scaling issues related to the Variant Call File format, VCF.
Every Two Months
Monday
13:00 UTC
1 Hour
This group meets to discuss scaling issues related to the Variant Call File format, VCF.
Every Two Months
Monday
21:00 UTC
1 Hour
Working meeting focussed on storing and accessing data in encrypted and authenticated states
Monthly
Tuesday
14:00 UTC
1 Hour
Working meeting focussed on focussed on Rust implementation work and benchmarking implementations.
Meets every eight weeks on a Wednesday at 5:00pm BST. Alternates with the other htsget meeting, which meets every eight weeks on a Tuesday at 10:00pm BST.
Every Two Months
Wednesday
17:00 UTC
1 Hour
Working meeting focused on focused on Rust implementation work and benchmarking implementations.
Meets every eight weeks on a Tuesday at 10:00pm BST. Alternates with the other htsget meeting, which takes place every eight weeks on a Wednesday at 5:00pm BST.
Every Two Months
Tuesday
22:00 UTC
1 Hour
Working meeting focused on generating identifiers from reference sequences and specifying an API to retrieve sequences, sub-sequences, and metadata
Bi-Weekly
Wednesday
14:00 UTC
1 Hour
Working meeting focused on endpoints for search and retrieval of processed RNA data.
Meets on the third Wednesday of the month.
Monthly
Wednesday
17:00 UTC
1 Hour
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Date
Title
15 Dec 2023
7 Nov 2023
19 Sep 2023
14 Sep 2023
14 Sep 2023
11 Mar 2023
11 Mar 2023
11 Mar 2023
11 Mar 2023
11 Mar 2023
11 Mar 2023
10 Mar 2023
25 Sep 2022
4 Jan 2022
4 Jan 2022
12 Dec 2020
8 Dec 2020
8 Dec 2020
8 Dec 2020
8 Dec 2020
8 Dec 2020
26 Apr 2019
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Don't see your name? Get in touch:
- Jeremy Adams
DNAstack - Shakuntala Baichoo
University of Mauritius - Dixie Baker
Martin, Blanck and Associates - Michael Baudis
University of Zurich - Edmon Begoli
Oak Ridge National Laboratory (ORNL) - Nicolas Bertin
Genome Institute of Singapore - James Bonfield
Wellcome Sanger Institute (WSI) - Guillaume Bourque
McGill University / Université McGill - David Bujold
McGill University / Université McGill - Daniel Cameron
Walter and Eliza Hall Institute of Medical Research - Timothe Cezard
EMBL's European Bioinformatics Institute (EBI) - Shu Hui Chen
NIH National Heart, Lung, and Blood Institute (NHLBI) - Guy Cochrane
Independent Contributor - Robert Davies
Wellcome Sanger Institute (WSI) - Richard Durbin
University of Cambridge - Yossi Farjoun
Lady Davis Institute - Mallory Freeberg
EMBL's European Bioinformatics Institute (EBI) - Kais Ghedira
Institut Pasteur de Tunis - Romain Gregoire
Canadian Centre for Computational Genomics - Roderic Guigo
Centre for Genomic Regulation - Sveinung Gundersen
Centre for Bioinformatics, University of Oslo - Yosr Hamdi
Institut Pasteur de Tunis - Reece Hart
MyOme - Muhammad Haseeb
EMBL's European Bioinformatics Institute (EBI) - Michael Hoffman
Princess Margaret Cancer Centre - Oliver Hofmann
University of Melbourne Centre for Cancer Research - David Jackson
Wellcome Sanger Institute (WSI) - Thomas Keane
EMBL's European Bioinformatics Institute (EBI) - Jerome Kelleher
University of Oxford - Rasko Leinonen
EMBL's European Bioinformatics Institute (EBI) - Anders Leung
Independent Contributor - Mike Lin
Independent Contributor - John Marshall
University of Glasgow - Emilio Palumbo
Centre for Genomic Regulation - Martin Pollard
Wellcome Sanger Institute (WSI) - Shaikh Farhan Rashid
University Health Network, Canadian Distributed Infrastructure for Genomics (CanDIG) - Emilio Righi
Centre for Genomic Regulation - Alexander Senf
Congenica - Nathan Sheffield
University of Virginia - Albert Smith
University of Michigan - Jing Su
Wellcome Sanger Institute (WSI) - Sean Upchurch
California Institute of Technology - Roman Valls Guimera
University of Melbourne Centre for Cancer Research - Zhenyu Zhang
University of Chicago