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 2k 627

  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 384

  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 1541 repositories
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv's past year of commit activity
    Python 208 BSD-3-Clause 83 101 33 Updated Sep 25, 2026
  • mccarroll-nf-recon Public
    broadinstitute/mccarroll-nf-recon's past year of commit activity
    0 0 0 0 Updated Sep 26, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp's past year of commit activity
    Jupyter Notebook 231 BSD-3-Clause 118 13 25 Updated Sep 26, 2026
  • via Public

    A new variant interpretation tool for the All of Us Researcher Workbench, leveraging linked genomic and phenotypic data to support clinical classification

    broadinstitute/via's past year of commit activity
    TypeScript 2 0 0 1 Updated Sep 26, 2026
  • SpliceAI-lookup Public

    Website for checking the SpliceAI, Pangolin, and other predictor scores for variant(s) of interest.

    broadinstitute/SpliceAI-lookup's past year of commit activity
    Python 34 MIT 9 10 0 Updated Sep 25, 2026
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal's past year of commit activity
    Vue 3 BSD-3-Clause 3 0 14 Updated Sep 25, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk's past year of commit activity
    Java 2,000 627 1,292 (8 issues need help) 165 Updated Sep 25, 2026
  • dig-aggregator-methods Public

    Monorepo of methods implemented for the Aggregator

    broadinstitute/dig-aggregator-methods's past year of commit activity
    Python 1 BSD-3-Clause 3 0 9 Updated Sep 25, 2026
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines's past year of commit activity
    Jupyter Notebook 152 BSD-3-Clause 24 95 (2 issues need help) 24 Updated Sep 25, 2026
  • dig-knowledge-graph Public
    broadinstitute/dig-knowledge-graph's past year of commit activity
    Python 0 1 2 0 Updated Sep 25, 2026
View all repositories