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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 2k 626

  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 385

  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 1536 repositories
  • haplograph Public
    broadinstitute/haplograph's past year of commit activity
    WDL 3 MIT 0 0 0 Updated Sep 13, 2026
  • 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 6 1 8 (1 issue needs help) 2 Updated Sep 13, 2026
  • exome-results-browsers Public

    Results browsers for case-control studies of psychiatric diseases done at the Broad Institute

    broadinstitute/exome-results-browsers's past year of commit activity
    TypeScript 12 BSD-3-Clause 4 15 10 Updated Sep 13, 2026
  • prefect Public Forked from PrefectHQ/prefect

    Prefect is a workflow orchestration framework for building resilient data pipelines in Python.

    broadinstitute/prefect's past year of commit activity
    Python 0 Apache-2.0 2,575 0 11 Updated Sep 13, 2026
  • genomeshader Public

    Visualization of biobank-scale genomic datasets.

    broadinstitute/genomeshader's past year of commit activity
    JavaScript 7 BSD-3-Clause 0 9 (1 issue needs help) 5 Updated Sep 13, 2026
  • martian Public Forked from martian-lang/martian

    Language and framework for high performance computational pipelines.

    broadinstitute/martian's past year of commit activity
    Go 0 MIT 31 0 2 Updated Sep 13, 2026
  • pyqtl Public

    Collection of analysis tools for quantitative trait loci

    broadinstitute/pyqtl's past year of commit activity
    Python 65 BSD-3-Clause 12 1 2 Updated Sep 13, 2026
  • genohype-docs Public

    Documentation site for the genohype genomic data toolkit ecosystem

    broadinstitute/genohype-docs's past year of commit activity
    Astro 0 0 0 9 Updated Sep 13, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp's past year of commit activity
    Jupyter Notebook 229 BSD-3-Clause 118 13 21 Updated Sep 13, 2026
  • warp-tools Public

    This repository contains all containers that WARP uses.

    broadinstitute/warp-tools's past year of commit activity
    Python 16 BSD-3-Clause 4 1 12 Updated Sep 13, 2026
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