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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 625

  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 1469 repositories
  • 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) 3 Updated Apr 13, 2026
  • pyqtl Public

    Collection of analysis tools for quantitative trait loci

    broadinstitute/pyqtl’s past year of commit activity
    Python 62 BSD-3-Clause 11 0 2 Updated Apr 13, 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 12, 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 12, 2026
  • ml4h Public
    broadinstitute/ml4h’s past year of commit activity
    Python 169 GPL-3.0 24 33 (1 issue needs help) 24 Updated Apr 12, 2026
  • Drop-seq-wdl Public
    broadinstitute/Drop-seq-wdl’s past year of commit activity
    WDL 0 MIT 0 1 0 Updated Apr 12, 2026
  • Himito Public
    broadinstitute/Himito’s past year of commit activity
    WDL 9 MIT 2 0 0 Updated Apr 12, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 225 BSD-3-Clause 116 7 21 Updated Apr 12, 2026
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 2 0 0 Updated Apr 12, 2026
  • permutect Public

    Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling

    broadinstitute/permutect’s past year of commit activity
    Python 12 Apache-2.0 2 10 1 Updated Apr 12, 2026
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