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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 631

  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 383

Repositories

Showing 10 of 1551 repositories
  • celldega Public

    Spatial and multiomic visualization and analysis library

    broadinstitute/celldega's past year of commit activity
    Jupyter Notebook 82 8 1 53 Updated Nov 6, 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 Nov 6, 2026
  • cheesemonger Public

    A storage system for large perturb seq data

    broadinstitute/cheesemonger's past year of commit activity
    Python 1 0 0 1 Updated Nov 6, 2026
  • Drop-seq Public

    Java tools for analyzing Drop-seq data

    broadinstitute/Drop-seq's past year of commit activity
    Jupyter Notebook 137 MIT 34 11 0 Updated Nov 5, 2026
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr's past year of commit activity
    Python 220 AGPL-3.0 97 50 12 Updated Nov 5, 2026
  • prefect Public Forked from PrefectHQ/prefect

    Prefect is a workflow orchestration framework for building resilient data pipelines in Python.

    broadinstitute/prefect's past year of commit activity
    Python 0 Apache-2.0 2,691 0 26 Updated Nov 5, 2026
  • PrimerCast Public

    Design tool for highly performant qPCR diagnostics.

    broadinstitute/PrimerCast's past year of commit activity
    Python 12 MIT 1 5 1 Updated Nov 6, 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 5, 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 5, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk's past year of commit activity
    Java 2,010 631 1,293 (8 issues need help) 171 Updated Nov 5, 2026
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