Repositories list

• va-spec

  Public
  An information model for representing variant annotations.

  Jupyter Notebook

  •

  Apache License 2.0

  •4•17•103•1•Updated Nov 27, 2024Nov 27, 2024

• vrs

  Public
  Extensible specification for representing and uniquely identifying biological sequence variation

  bioinformaticsgenomicsvariation

  Jupyter Notebook

  •

  Apache License 2.0

  •34•80•22•3•Updated Nov 27, 2024Nov 27, 2024

• cat-vrs

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

  Makefile

  •

  Apache License 2.0

  •2•1•6•0•Updated Nov 27, 2024Nov 27, 2024

• gks-metaschema

  Public
  Tools and scripts for parsing the GKS standards metaschemas

  Python

  •

  Apache License 2.0

  •3•0•6•1•Updated Nov 27, 2024Nov 27, 2024

• va-spec-python

  Public
  GA4GH Variation Annotation Python Implementation

  Python

  •

  Apache License 2.0

  •1•0•1•0•Updated Nov 26, 2024Nov 26, 2024

• cat-vrs-python

  Public
  GA4GH Categorical Variation Representation Python Implementation

  Python

  •

  Apache License 2.0

  •3•0•1•0•Updated Nov 26, 2024Nov 26, 2024

• 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•6•3•Updated Nov 26, 2024Nov 26, 2024

• gks-core

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

  Python

  •

  Apache License 2.0

  •0•2•1•1•Updated Nov 26, 2024Nov 26, 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

  7•8•16•2•Updated Nov 25, 2024Nov 25, 2024

• refget

  Public
  GA4GH Refget specifications docs

  collectiondigestfasta+ 1sequence

  HTML

  •7•14•22•2•Updated Nov 20, 2024Nov 20, 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 Nov 20, 2024Nov 20, 2024

• fasp-clients

  Public
  a place for client code from the FASP effort

  Python

  •

  Apache License 2.0

  •3•2•6•0•Updated Nov 17, 2024Nov 17, 2024

• vrs-python

  Public
  GA4GH Variation Representation Python Implementation

  bioinformaticsgenomicsga4gh

  Python

  •

  Apache License 2.0

  •27•51•37•3•Updated Nov 15, 2024Nov 15, 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

• w3id.org

  Public
  Forwarding links and rewrite rules for w3id.org

  HTML

  •1.2k•3•0•0•Updated Nov 15, 2024Nov 15, 2024

• task-execution-schemas

  Public
  Apache License 2.0

  •29•82•42•12•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

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

• 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 Nov 8, 2024Nov 8, 2024

• gks-portal

  Public
  MIT License

  •1•0•9•0•Updated Nov 7, 2024Nov 7, 2024

• tool-registry-service-schemas

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

  apitoolworkflow+ 3wdlga4ghcwl

  Shell

  •

  Apache License 2.0

  •18•30•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•22•8•5•Updated Oct 28, 2024Oct 28, 2024

• ga4gh-testbed-api

  Public
  GA4GH-wide testbed infrastructure for hosting testbed reports

  Java

  •1•1•8•1•Updated Oct 22, 2024Oct 22, 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

  •38•82•51•5•Updated Sep 28, 2024Sep 28, 2024

• pedigree_family_history_terminology

  Public
  Java

  •

  Apache License 2.0

  •6•5•11•0•Updated Sep 17, 2024Sep 17, 2024

• ga4gh-testbed-ui

  Public
  Web UI for the GA4GH Testbed Reporting service

  testbed

  JavaScript

  •

  Apache License 2.0

  •1•2•0•2•Updated Sep 10, 2024Sep 10, 2024

• gks2clinvar

  Public
  A submission tool for submitting to the ClinVar Submission API using GA4GH GKS data

  Apache License 2.0

  •0•0•9•4•Updated Sep 4, 2024Sep 4, 2024

• pedigree-tools

  Public
  JavaScript

  •1•1•4•9•Updated Aug 21, 2024Aug 21, 2024