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 619

  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 375

Repositories

Showing 10 of 1419 repositories
  • gnomad_qc Public
    broadinstitute/gnomad_qc’s past year of commit activity
    Jupyter Notebook 68 BSD-3-Clause 28 6 10 Updated Nov 17, 2025
  • seqr-helm Public

    Helm charts for the seqr project

    broadinstitute/seqr-helm’s past year of commit activity
    Python 3 BSD-3-Clause 2 5 1 Updated Nov 17, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 21 1 1 52 Updated Nov 17, 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 22 19 6 Updated Nov 17, 2025
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 219 BSD-3-Clause 111 6 9 Updated Nov 17, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 195 AGPL-3.0 91 50 5 Updated Nov 17, 2025
  • ddp-study-server Public

    Pepper Study Server

    broadinstitute/ddp-study-server’s past year of commit activity
    Java 8 BSD-3-Clause 7 1 2 Updated Nov 17, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,876 619 1,271 (8 issues need help) 144 Updated Nov 17, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 26 BSD-3-Clause 4 0 5 Updated Nov 17, 2025
  • dsp-appsec-infrastructure-apps Public

    This repository hosts DSP AppSec internal infrastructure apps deployed in GKE.

    broadinstitute/dsp-appsec-infrastructure-apps’s past year of commit activity
    Python 7 BSD-3-Clause 2 0 5 Updated Nov 17, 2025
View all repositories