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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 2k 630

  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 382

Repositories

Showing 10 of 1542 repositories
  • gnomad-browser Public

    Explore gnomAD datasets on the web

    broadinstitute/gnomad-browser's past year of commit activity
    TypeScript 91 MIT 56 173 (4 issues need help) 19 Updated Oct 15, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk's past year of commit activity
    Java 2,005 630 1,292 (8 issues need help) 169 Updated Oct 15, 2026
  • dsp-appsec-trivy-action Public

    DSP Appsec team action, which checks if a Dockerfile is using our base "blessed" image, if yes, no scan is needed, otherwise this action will build image and scan it with Trivy tool.

    broadinstitute/dsp-appsec-trivy-action's past year of commit activity
    2 2 0 4 Updated Oct 15, 2026
  • 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 20 MIT 2 0 0 Updated Oct 15, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp's past year of commit activity
    Jupyter Notebook 232 BSD-3-Clause 118 13 31 Updated Oct 15, 2026
  • PrimerCast Public

    Design tool for highly performant qPCR diagnostics.

    broadinstitute/PrimerCast's past year of commit activity
    Python 12 MIT 1 5 0 Updated Oct 14, 2026
  • str-analysis Public

    Scripts and utilities for analyzing tandem repeats (TRs).

    broadinstitute/str-analysis's past year of commit activity
    Python 53 MIT 15 0 0 Updated Oct 14, 2026
  • site-shell Public
    broadinstitute/site-shell's past year of commit activity
    JavaScript 1 BSD-3-Clause 0 0 0 Updated Oct 14, 2026
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal's past year of commit activity
    Vue 3 BSD-3-Clause 4 0 8 Updated Oct 14, 2026
  • celldega Public

    Spatial and multiomic visualization and analysis library

    broadinstitute/celldega's past year of commit activity
    Jupyter Notebook 66 7 1 61 Updated Oct 14, 2026
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