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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 624

  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 382

  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 381

Repositories

Showing 10 of 1472 repositories
  • SpliceAI-lookup-dev Public

    dev. version of the spliceai-lookup.broadinstitute.org website

    broadinstitute/SpliceAI-lookup-dev’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Apr 19, 2026
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines’s past year of commit activity
    Jupyter Notebook 151 BSD-3-Clause 25 95 (2 issues need help) 25 Updated Apr 19, 2026
  • popout Public

    GPU-accelerated local ancestry inference at biobank scale, no reference panel required.

    broadinstitute/popout’s past year of commit activity
    Python 2 0 0 0 Updated Apr 19, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 202 BSD-3-Clause 76 98 30 Updated Apr 19, 2026
  • Drop-seq-wdl Public
    broadinstitute/Drop-seq-wdl’s past year of commit activity
    WDL 0 MIT 0 1 0 Updated Apr 19, 2026
  • Himito Public
    broadinstitute/Himito’s past year of commit activity
    WDL 9 MIT 2 0 0 Updated Apr 19, 2026
  • BE3D Public

    BE3D public repository

    broadinstitute/BE3D’s past year of commit activity
    Python 1 MIT 0 2 0 Updated Apr 18, 2026
  • qprimer_designer Public

    Design tool for highly performant qPCR diagnostics.

    broadinstitute/qprimer_designer’s past year of commit activity
    Python 6 MIT 1 5 0 Updated Apr 18, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,937 624 1,284 (8 issues need help) 145 Updated Apr 18, 2026
  • ml4h Public
    broadinstitute/ml4h’s past year of commit activity
    Python 169 GPL-3.0 24 33 (1 issue needs help) 25 Updated Apr 18, 2026
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