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 622

  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 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 1k 377

Repositories

Showing 10 of 1440 repositories
  • lrma-aou2-panel-creation Public Forked from broadinstitute/lrma-aou1-panel-creation

    Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 2 long-reads callset.

    broadinstitute/lrma-aou2-panel-creation’s past year of commit activity
    Java 0 2 0 2 Updated Jan 21, 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 8 Updated Jan 21, 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 10 Updated Jan 21, 2026
  • gnomad_qc Public
    broadinstitute/gnomad_qc’s past year of commit activity
    Jupyter Notebook 68 BSD-3-Clause 29 6 14 Updated Jan 21, 2026
  • ml4h Public
    broadinstitute/ml4h’s past year of commit activity
    Python 163 GPL-3.0 29 32 (1 issue needs help) 26 Updated Jan 21, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 224 BSD-3-Clause 112 6 10 Updated Jan 21, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 200 BSD-3-Clause 76 94 30 Updated Jan 21, 2026
  • starrynight Public

    A toolkit for processing, analyzing, and managing optical pooled screening (OPS) image data.

    broadinstitute/starrynight’s past year of commit activity
    Python 9 BSD-3-Clause 5 0 7 Updated Jan 21, 2026
  • exome-results-browsers Public

    Results browsers for case-control studies of psychiatric diseases done at the Broad Institute

    broadinstitute/exome-results-browsers’s past year of commit activity
    JavaScript 11 BSD-3-Clause 4 8 7 Updated Jan 21, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,898 622 1,273 (8 issues need help) 143 Updated Jan 21, 2026
View all repositories

Most used topics

Loading…