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Broad Institute

Broad Institute of MIT and Harvard

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  1. gatk gatk Public

    Official code repository for GATK versions 4 and up

    Java 1.8k 609

  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 379

  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 373

Repositories

Showing 10 of 1412 repositories
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 25 BSD-3-Clause 4 0 5 Updated Aug 12, 2025
  • warp-tools Public

    This repository contains all containers that WARP uses.

    broadinstitute/warp-tools’s past year of commit activity
    Python 10 BSD-3-Clause 2 1 13 Updated Aug 12, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 193 AGPL-3.0 90 55 2 Updated Aug 12, 2025
  • cromwell Public

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

    broadinstitute/cromwell’s past year of commit activity
    Scala 1,027 BSD-3-Clause 373 755 54 Updated Aug 12, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 191 BSD-3-Clause 77 87 27 Updated Aug 12, 2025
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 9 BSD-3-Clause 5 0 19 Updated Aug 12, 2025
  • depmap_omics Public

    What you need to process the Quarterly DepMap-Omics releases from Terra

    broadinstitute/depmap_omics’s past year of commit activity
    HTML 119 23 3 3 Updated Aug 12, 2025
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 215 BSD-3-Clause 109 5 12 Updated Aug 12, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,833 609 1,261 (8 issues need help) 140 Updated Aug 12, 2025
  • PANOPLY Public

    Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)

    broadinstitute/PANOPLY’s past year of commit activity
    R 37 16 0 1 Updated Aug 12, 2025
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