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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 630

  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 387

  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 384

Repositories

Showing 10 of 1555 repositories
  • warp-sandbox-podman Public
    broadinstitute/warp-sandbox-podman's past year of commit activity
    Go 0 0 0 9 Updated Nov 13, 2026
  • perturb-seq-depmap-public Public

    Dissecting context-dependent cancer vulnerabilities using Perturb-seq. DepMap's Perturb-seq pilot in 16 cell lines

    broadinstitute/perturb-seq-depmap-public's past year of commit activity
    Python 1 0 0 12 Updated Nov 13, 2026
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal's past year of commit activity
    Vue 3 BSD-3-Clause 4 0 7 Updated Nov 13, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk's past year of commit activity
    Java 2,012 630 1,294 (8 issues need help) 178 Updated Nov 13, 2026
  • str-analysis Public

    Scripts and utilities for analyzing tandem repeats (TRs).

    broadinstitute/str-analysis's past year of commit activity
    Python 53 MIT 15 0 0 Updated Nov 13, 2026
  • gnomad-constraint Public
    broadinstitute/gnomad-constraint's past year of commit activity
    Python 5 BSD-3-Clause 1 2 8 Updated Nov 13, 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 9 Updated Nov 13, 2026
  • mccarroll_nextflow Public

    Nextflow workflows for BICAN scRNA processing

    broadinstitute/mccarroll_nextflow's past year of commit activity
    Nextflow 2 MIT 0 10 2 Updated Nov 13, 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 6 Updated Nov 12, 2026
  • tgg-rnaseq-dashboard Public

    An RNA-seq dashboard to integrate RNA-seq analyses with DNA variants.

    broadinstitute/tgg-rnaseq-dashboard's past year of commit activity
    TypeScript 0 0 0 0 Updated Nov 12, 2026
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