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@broadinstitute

Broad Institute

Broad Institute of MIT and Harvard

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  1. gatk gatk Public

    Official code repository for GATK versions 4 and up

    Java 2k 628

  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
  • celldega Public

    Spatial and multiomic visualization and analysis library

    broadinstitute/celldega's past year of commit activity
    Jupyter Notebook 60 7 1 60 Updated Oct 3, 2026
  • geneset-extractor-dev Public

    Geneset Extractor Development

    broadinstitute/geneset-extractor-dev's past year of commit activity
    Python 0 MIT 6 2 8 Updated Oct 3, 2026
  • mccarroll_nextflow Public

    Nextflow workflows for BICAN scRNA processing

    broadinstitute/mccarroll_nextflow's past year of commit activity
    Nextflow 2 MIT 0 18 2 Updated Oct 3, 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 2 1 7 Updated Oct 2, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk's past year of commit activity
    Java 2,004 628 1,292 (8 issues need help) 168 Updated Oct 2, 2026
  • cds-daintree Public
    broadinstitute/cds-daintree's past year of commit activity
    Python 1 2 0 2 Updated Oct 2, 2026
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal's past year of commit activity
    Vue 3 BSD-3-Clause 4 0 13 Updated Oct 2, 2026
  • juniper Public
    broadinstitute/juniper's past year of commit activity
    Java 11 BSD-3-Clause 5 0 20 Updated Oct 2, 2026
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr's past year of commit activity
    Python 219 AGPL-3.0 97 47 9 Updated Oct 2, 2026
  • ml4h Public
    broadinstitute/ml4h's past year of commit activity
    Python 181 GPL-3.0 12 33 (1 issue needs help) 27 Updated Oct 2, 2026
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