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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 1.9k 622

  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 382

  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 378

Repositories

Showing 10 of 1431 repositories
  • gnomad_qc Public
    broadinstitute/gnomad_qc’s past year of commit activity
    Jupyter Notebook 68 BSD-3-Clause 28 6 10 Updated Dec 18, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 197 AGPL-3.0 92 50 5 Updated Dec 18, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 198 BSD-3-Clause 75 93 26 Updated Dec 18, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 22 1 1 49 Updated Dec 18, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,894 622 1,271 (8 issues need help) 143 Updated Dec 18, 2025
  • str-analysis Public

    Scripts and utilities related to analyzing tandem repeats (TRs).

    broadinstitute/str-analysis’s past year of commit activity
    Python 41 MIT 10 0 0 Updated Dec 18, 2025
  • pattern-storybook Public
    broadinstitute/pattern-storybook’s past year of commit activity
    Vue 2 0 0 2 Updated Dec 18, 2025
  • MicroSplit-reproducibility Public Forked from CAREamics/MicroSplit-reproducibility

    Notebooks, scripts and utilities to reproduce MicroSplit

    broadinstitute/MicroSplit-reproducibility’s past year of commit activity
    Python 0 BSD-3-Clause 5 0 0 Updated Dec 18, 2025
  • permutect Public

    Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling

    broadinstitute/permutect’s past year of commit activity
    Python 5 1 10 2 Updated Dec 18, 2025
  • openidc-proxy Public

    Apache proxy with authentication or authorization based on mod_auth_openidc and mod_auth_ldap

    broadinstitute/openidc-proxy’s past year of commit activity
    Shell 5 BSD-3-Clause 1 0 4 Updated Dec 18, 2025
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