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@broadinstitute

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 2k 631

  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 386

  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 382

Repositories

Showing 10 of 1548 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 15 Apache-2.0 2 8 1 Updated Oct 27, 2026
  • via Public

    A new variant interpretation tool for the All of Us Researcher Workbench, leveraging linked genomic and phenotypic data to support clinical classification

    broadinstitute/via's past year of commit activity
    TypeScript 2 0 0 4 Updated Oct 27, 2026
  • koina Public Forked from wilhelm-lab/koina

    Democratizing ML in proteomics

    broadinstitute/koina's past year of commit activity
    Jupyter Notebook 0 Apache-2.0 30 0 18 Updated Oct 27, 2026
  • BE3D Public

    BE3D public repository

    broadinstitute/BE3D's past year of commit activity
    Python 1 MIT 1 3 10 Updated Oct 27, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp's past year of commit activity
    Jupyter Notebook 232 BSD-3-Clause 118 13 28 Updated Oct 26, 2026
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr's past year of commit activity
    Python 220 AGPL-3.0 97 49 10 Updated Oct 26, 2026
  • gnomad-browser Public

    Explore gnomAD datasets on the web

    broadinstitute/gnomad-browser's past year of commit activity
    TypeScript 91 MIT 55 172 (4 issues need help) 17 Updated Oct 26, 2026
  • cellpainting-gallery-metadata Public

    Project to create metadata that is harmonized across the Cell Painting Gallery

    broadinstitute/cellpainting-gallery-metadata's past year of commit activity
    Jupyter Notebook 5 BSD-3-Clause 0 4 0 Updated Oct 26, 2026
  • mccarroll_tw_clp Public

    Command-line wrappers for twcli with validation

    broadinstitute/mccarroll_tw_clp's past year of commit activity
    Python 0 MIT 0 0 3 Updated Oct 26, 2026
  • mccarroll-scrna-aggregation Public

    A nextflow workflow that aggregates

    broadinstitute/mccarroll-scrna-aggregation's past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Oct 26, 2026
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