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 1.8k 604

  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 373

  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 361

Repositories

Showing 10 of 1375 repositories
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 9 BSD-3-Clause 5 0 11 Updated Apr 16, 2025
  • 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 Apr 16, 2025
  • 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 20 25 4 Updated Apr 16, 2025
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 211 BSD-3-Clause 102 5 12 Updated Apr 16, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,792 604 1,244 (8 issues need help) 139 Updated Apr 16, 2025
  • broad-epi-utils Public

    Python packages with python scripts for QA/QC of single-cell multi-omic and ChIP assays.

    broadinstitute/broad-epi-utils’s past year of commit activity
    Jinja 0 MIT 0 0 0 Updated Apr 15, 2025
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 8 BSD-2-Clause 1 0 8 Updated Apr 15, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 1 1 0 Updated Apr 15, 2025
  • cromwell Public

    Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

    broadinstitute/cromwell’s past year of commit activity
    Scala 1,012 BSD-3-Clause 361 746 49 Updated Apr 15, 2025
  • jati Public

    DSL support library for Rust

    broadinstitute/jati’s past year of commit activity
    Rust 1 BSD-3-Clause 0 0 0 Updated Apr 15, 2025
View all repositories