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 606

  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 378

  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 369

Repositories

Showing 10 of 1391 repositories
  • dcc_pigean_flask Public

    Flask server for the Pigean method

    broadinstitute/dcc_pigean_flask’s past year of commit activity
    Python 0 0 3 8 Updated Jul 3, 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 6 Updated Jul 3, 2025
  • monorepo Public

    Compendium of tools for the Imaging Platform

    broadinstitute/monorepo’s past year of commit activity
    Python 12 BSD-3-Clause 3 7 0 Updated Jul 3, 2025
  • Drop-seq Public

    Java tools for analyzing Drop-seq data

    broadinstitute/Drop-seq’s past year of commit activity
    Java 128 MIT 35 17 1 Updated Jul 3, 2025
  • stp_segmentation_wdl Public
    broadinstitute/stp_segmentation_wdl’s past year of commit activity
    WDL 0 0 0 0 Updated Jul 3, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 189 BSD-3-Clause 75 83 29 Updated Jul 3, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,817 606 1,257 (8 issues need help) 136 Updated Jul 2, 2025
  • str-analysis Public

    Scripts and utilities related to analyzing short tandem repeats (STRs).

    broadinstitute/str-analysis’s past year of commit activity
    Python 38 MIT 9 0 0 Updated Jul 2, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 25 BSD-3-Clause 4 0 5 Updated Jul 3, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 9 0 1 35 Updated Jul 2, 2025
View all repositories