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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 1.9k 623

  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 1.1k 381

  3. cromwell cromwell Public

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

    Scala 1.1k 378

Repositories

Showing 10 of 1449 repositories
  • permutect Public

    Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling

    broadinstitute/permutect’s past year of commit activity
    Python 9 1 10 2 Updated Feb 24, 2026
  • bits-appengine Public

    BITS AppEngine Python Package

    broadinstitute/bits-appengine’s past year of commit activity
    Python 0 0 0 1 Updated Feb 24, 2026
  • 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 1,053 BSD-3-Clause 378 759 50 Updated Feb 24, 2026
  • seqr-loading-pipelines Public

    hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

    broadinstitute/seqr-loading-pipelines’s past year of commit activity
    Python 23 MIT 23 20 5 Updated Feb 24, 2026
  • palantir-workflows Public

    Utility workflows for the DSP hydro.gen team (formerly palantir)

    broadinstitute/palantir-workflows’s past year of commit activity
    WDL 26 BSD-3-Clause 11 4 4 Updated Feb 24, 2026
  • bican-mccarroll-manuscript1 Public

    Scripts used to process data for the first McCarroll lab BICAN manuscript

    broadinstitute/bican-mccarroll-manuscript1’s past year of commit activity
    R 0 MIT 0 0 2 Updated Feb 24, 2026
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 73 30 21 19 Updated Feb 24, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 225 BSD-3-Clause 112 6 11 Updated Feb 23, 2026
  • gnomad-browser Public

    Explore gnomAD datasets on the web

    broadinstitute/gnomad-browser’s past year of commit activity
    TypeScript 86 MIT 49 167 (3 issues need help) 14 Updated Feb 23, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,912 623 1,279 (8 issues need help) 148 Updated Feb 24, 2026
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