Skip to content
@broadinstitute

Broad Institute

Broad Institute of MIT and Harvard

Pinned Loading

  1. gatk gatk Public

    Official code repository for GATK versions 4 and up

    Java 1.9k 621

  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 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 1k 376

Repositories

Showing 10 of 1427 repositories
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 197 AGPL-3.0 92 51 9 Updated Dec 8, 2025
  • monorepo Public

    Compendium of tools for the Imaging Platform

    broadinstitute/monorepo’s past year of commit activity
    Python 15 BSD-3-Clause 3 3 2 Updated Dec 8, 2025
  • sherlock Public

    DSP DevOps's deployment source-of-truth service

    broadinstitute/sherlock’s past year of commit activity
    Go 1 BSD-3-Clause 0 0 7 Updated Dec 8, 2025
  • 2025_varchamp_snakemake Public
    broadinstitute/2025_varchamp_snakemake’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Dec 8, 2025
  • str-analysis Public

    Scripts and utilities related to analyzing tandem repeats (TRs).

    broadinstitute/str-analysis’s past year of commit activity
    Python 41 MIT 10 0 0 Updated Dec 8, 2025
  • trexplorer-catalog Public

    Genome-wide TR catalog and variation clusters described in [Weisburd, Dolzhenko, et al. 2024]

    broadinstitute/trexplorer-catalog’s past year of commit activity
    Python 17 MIT 1 0 0 Updated Dec 7, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,889 621 1,271 (8 issues need help) 146 Updated Dec 7, 2025
  • 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 0 Updated Dec 7, 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 11 4 3 Updated Dec 7, 2025
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines’s past year of commit activity
    Jupyter Notebook 150 BSD-3-Clause 25 95 (2 issues need help) 25 Updated Dec 6, 2025
View all repositories