Skip to content
@broadinstitute

Broad Institute

Broad Institute of MIT and Harvard

Pinned Loading

  1. gatk gatk Public

    Official code repository for GATK versions 4 and up

    Java 1.9k 615

  2. picard picard Public

    A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

    Java 1k 380

  3. cromwell cromwell Public

    Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

    Scala 1k 374

Repositories

Showing 10 of 1410 repositories
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 194 BSD-3-Clause 77 88 31 Updated Oct 1, 2025
  • gnomad-browser Public

    Explore gnomAD datasets on the web

    broadinstitute/gnomad-browser’s past year of commit activity
    TypeScript 85 MIT 49 165 (3 issues need help) 9 Updated Oct 1, 2025
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 215 BSD-3-Clause 111 6 10 Updated Sep 30, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 25 BSD-3-Clause 4 0 3 Updated Sep 30, 2025
  • protigy-v2 Public

    ProTIGY - Proteogenomics Toolset for Integrative Data Analysis

    broadinstitute/protigy-v2’s past year of commit activity
    R 1 BSD-3-Clause 0 14 0 Updated Sep 30, 2025
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 8 BSD-2-Clause 1 0 8 Updated Sep 30, 2025
  • GeneTEA Public

    Gene-Term Enrichment Analysis (GeneTEA)

    broadinstitute/GeneTEA’s past year of commit activity
    Jupyter Notebook 3 2 0 6 Updated Sep 30, 2025
  • gnomad_qc Public
    broadinstitute/gnomad_qc’s past year of commit activity
    Jupyter Notebook 68 BSD-3-Clause 27 6 9 Updated Sep 30, 2025
  • gnomad_methods Public

    Hail helper functions for the gnomAD project and Translational Genomics Group

    broadinstitute/gnomad_methods’s past year of commit activity
    Python 96 MIT 30 9 8 Updated Sep 30, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 194 AGPL-3.0 90 48 5 Updated Sep 30, 2025
View all repositories