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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 619

  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 380

  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 375

Repositories

Showing 10 of 1418 repositories
  • viral-core Public

    viral-ngs: read QC, barcode metrics, spike-in metrics, Illumina metrics and demux

    broadinstitute/viral-core’s past year of commit activity
    Python 4 1 11 2 Updated Nov 9, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 195 AGPL-3.0 90 53 5 Updated Nov 9, 2025
  • 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 22 21 8 Updated Nov 9, 2025
  • colab-repeat-finder Public

    A tool that finds perfect and nearly-perfect repeats

    broadinstitute/colab-repeat-finder’s past year of commit activity
    Python 2 MIT 0 1 0 Updated Nov 9, 2025
  • 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 10 4 3 Updated Nov 9, 2025
  • celldega_Visium_HD_3prime_Mouse_Embryo Public
    broadinstitute/celldega_Visium_HD_3prime_Mouse_Embryo’s past year of commit activity
    0 0 0 0 Updated Nov 9, 2025
  • backstage Public

    Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)

    broadinstitute/backstage’s past year of commit activity
    TypeScript 2 0 1 3 Updated Nov 8, 2025
  • poolq Public

    The Genetic Perturbation Platform's tool for deconvoluting and quantifying the results of pooled screens

    broadinstitute/poolq’s past year of commit activity
    Scala 5 1 8 (1 issue needs help) 1 Updated Nov 8, 2025
  • fiss-mcp Public

    MCP server for Terra

    broadinstitute/fiss-mcp’s past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Nov 8, 2025
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 67 29 24 18 Updated Nov 8, 2025
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