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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 622

  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 379

Repositories

Showing 10 of 1447 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 8 1 10 2 Updated Feb 13, 2026
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 200 AGPL-3.0 93 41 8 Updated Feb 13, 2026
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 72 30 21 19 Updated Feb 13, 2026
  • lrma-aou2-panel-creation Public Forked from broadinstitute/lrma-aou1-panel-creation

    Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 2 long-reads callset.

    broadinstitute/lrma-aou2-panel-creation’s past year of commit activity
    Java 0 2 0 2 Updated Feb 13, 2026
  • haplograph Public
    broadinstitute/haplograph’s past year of commit activity
    WDL 3 MIT 0 0 0 Updated Feb 13, 2026
  • BE3D Public

    BE3D public repository

    broadinstitute/BE3D’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Feb 13, 2026
  • genomeshader Public

    Visualization of biobank-scale genomic datasets.

    broadinstitute/genomeshader’s past year of commit activity
    JavaScript 4 BSD-3-Clause 0 7 (2 issues need help) 3 Updated Feb 13, 2026
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    TypeScript 8 BSD-2-Clause 1 1 8 Updated Feb 13, 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 3 Updated Feb 13, 2026
  • broad-nnfc-hiPSC-to-EC Public
    broadinstitute/broad-nnfc-hiPSC-to-EC’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Feb 13, 2026
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