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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 1.9k 623

  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 381

  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 378

Repositories

Showing 10 of 1449 repositories
  • seqr-helm Public

    Helm charts for the seqr project

    broadinstitute/seqr-helm’s past year of commit activity
    Python 3 BSD-3-Clause 5 5 2 Updated Feb 24, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 201 BSD-3-Clause 76 97 26 Updated Feb 24, 2026
  • 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 23 20 5 Updated Feb 24, 2026
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 73 30 21 19 Updated Feb 24, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 225 BSD-3-Clause 112 6 12 Updated Feb 24, 2026
  • MicroSplit-reproducibility Public Forked from CAREamics/MicroSplit-reproducibility

    Notebooks, scripts and utilities to reproduce MicroSplit

    broadinstitute/MicroSplit-reproducibility’s past year of commit activity
    Python 0 BSD-3-Clause 5 0 9 Updated Feb 24, 2026
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    TypeScript 8 BSD-2-Clause 1 1 9 Updated Feb 24, 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 5 1 8 (1 issue needs help) 1 Updated Feb 24, 2026
  • orsp-pub Public

    Public ORSP Compliance Portal

    broadinstitute/orsp-pub’s past year of commit activity
    JavaScript 3 BSD-3-Clause 0 0 25 Updated Feb 24, 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 9 1 10 2 Updated Feb 24, 2026
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