Repositories list

• vrs-python

  Public
  GA4GH Variation Representation Python Implementation

  bioinformaticsgenomicsga4gh

  Python

  •

  Apache License 2.0

  •29•53•44•6•Updated Feb 7, 2025Feb 7, 2025

• cat-vrs

  Public
  A terminology and data model for describing categorical variation concepts.

  Makefile

  •

  Apache License 2.0

  •2•3•10•0•Updated Feb 7, 2025Feb 7, 2025

• gks-core

  Public
  Common classes and schemas used by all GKS specifications (ie. VR, VA, etc..)

  Python

  •

  Apache License 2.0

  •0•2•4•2•Updated Feb 6, 2025Feb 6, 2025

• schema-registry

  Public
  Repository of schemas to be loaded by the schema registry API

  schema-registry

  Apache License 2.0

  •0•0•2•1•Updated Feb 4, 2025Feb 4, 2025

• htsget-compliance

  Public
  Compliance testing for htsget deployments

  Python

  •

  Apache License 2.0

  •2•1•0•1•Updated Feb 3, 2025Feb 3, 2025

• va-spec-python

  Public
  GA4GH Variation Annotation Python Implementation

  bioinformaticsgenomicsga4gh

  Python

  •

  Apache License 2.0

  •1•1•5•1•Updated Jan 31, 2025Jan 31, 2025

• data-repository-service-schemas

  Public
  A repository for the schemas used for the Data Repository Service.

  Apache License 2.0

  •53•60•64•23•Updated Jan 28, 2025Jan 28, 2025

• gks-portal

  Public
  MIT License

  •1•0•5•0•Updated Jan 24, 2025Jan 24, 2025

• cat-vrs-python

  Public
  GA4GH Categorical Variation Representation Python Implementation

  bioinformaticsgenomicsga4gh

  Python

  •

  Apache License 2.0

  •3•1•1•0•Updated Jan 23, 2025Jan 23, 2025

• quality-control-wgs

  Public
  Home for the GA4GH Quality Control of Whole Genome Sequencing metrics and reference implementations

  Jupyter Notebook

  •

  Apache License 2.0

  •3•14•4•2•Updated Jan 21, 2025Jan 21, 2025

• va-spec

  Public
  An information model for representing variant annotations.

  Jupyter Notebook

  •

  Apache License 2.0

  •5•18•120•4•Updated Jan 15, 2025Jan 15, 2025

• refget

  Public
  GA4GH Refget specifications docs

  collectiondigestfasta+ 1sequence

  HTML

  •7•14•17•0•Updated Jan 9, 2025Jan 9, 2025

• gk-pilot

  Public
  A pilot implementation of GKS Work Stream specifications.

  Makefile

  •

  Apache License 2.0

  •2•1•11•2•Updated Jan 8, 2025Jan 8, 2025

• vrs

  Public
  Extensible specification for representing and uniquely identifying biological sequence variation

  bioinformaticsgenomicsvariation

  Jupyter Notebook

  •

  Apache License 2.0

  •36•84•22•4•Updated Jan 8, 2025Jan 8, 2025

• w3id.org

  Public
  Forwarding links and rewrite rules for w3id.org

  HTML

  •1.3k•3•0•0•Updated Dec 19, 2024Dec 19, 2024

• fasp-scripts

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •6•11•9•0•Updated Dec 18, 2024Dec 18, 2024

• ga4gh-starter-kit-drs

  Public
  Open, extensible server implementation of the GA4GH Data Repository Service (DRS) specification

  starter-kit

  Java

  •

  Apache License 2.0

  •7•4•9•1•Updated Dec 17, 2024Dec 17, 2024

• ga4gh-testbed-api

  Public
  GA4GH-wide testbed infrastructure for hosting testbed reports

  Java

  •1•1•8•0•Updated Dec 17, 2024Dec 17, 2024

• TASC

  Public
  TASC aids the harmonisation of aspects of GA4GH's various products that would otherwise prevent different products from being used together conveniently.

  interoperabilityharmonisationtechnical-alignment

  8•9•15•3•Updated Dec 5, 2024Dec 5, 2024

• fasp-clients

  Public
  a place for client code from the FASP effort

  Python

  •

  Apache License 2.0

  •4•2•6•0•Updated Nov 29, 2024Nov 29, 2024

• gks-metaschema

  Public
  Tools and scripts for parsing the GKS standards metaschemas

  Python

  •

  Apache License 2.0

  •3•0•6•0•Updated Nov 27, 2024Nov 27, 2024

• ga4gh-starter-kit-common

  Public
  Common utils library for GA4GH Starter Kit web services

  starter-kit

  Java

  •

  Apache License 2.0

  •2•1•6•2•Updated Nov 15, 2024Nov 15, 2024

• task-execution-schemas

  Public
  Apache License 2.0

  •29•83•39•11•Updated Nov 15, 2024Nov 15, 2024

• Get-Started-with-GA4GH-APIs

  Public
  ISMB 2022 tutorial on FASP and Starter Kit

  Jupyter Notebook

  •

  Apache License 2.0

  •2•6•5•1•Updated Nov 12, 2024Nov 12, 2024

• tool-registry-service-schemas

  Public
  APIs for discovering genomics tools, their metadata and their containers

  apitoolworkflow+ 3wdlga4ghcwl

  Shell

  •

  Apache License 2.0

  •18•31•25•1•Updated Oct 29, 2024Oct 29, 2024

• data-security

  Public
  This is the repository for the GA4GH Data Security Work Stream, containing AAI and DSIP.

  Python

  •16•23•8•5•Updated Oct 28, 2024Oct 28, 2024

• ga4gh-bed

  Public archive
  The browser extensible data (BED) file format describes genomic intervals on chromosomes or scaffolds

  Apache License 2.0

  •2•0•1•2•Updated Oct 17, 2024Oct 17, 2024

• gks-starter-repo

  Public
  A starting point to copy and use for teams wishing to quickly define their own schema extensions and profiles to the VA, Cat-VRS or VRS schemas.

  Python

  •

  Apache License 2.0

  •1•1•0•0•Updated Oct 11, 2024Oct 11, 2024

• ga4gh-testbed-lib

  Public
  Python library for creating GA4GH testbed reports according to a harmonized, cross-workstream schema

  testbed

  Python

  •

  Apache License 2.0

  •1•1•2•1•Updated Sep 30, 2024Sep 30, 2024

• workflow-execution-service-schemas

  Public
  The WES API is a standard way to run and manage portable workflows.

  workflowwdlga4gh+ 1cwl

  Apache License 2.0

  •39•83•51•5•Updated Sep 28, 2024Sep 28, 2024