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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

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Showing 10 of 1432 repositories
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 70 30 21 18 Updated Dec 24, 2025
  • str-analysis Public

    Scripts and utilities for analyzing tandem repeats (TRs).

    broadinstitute/str-analysis’s past year of commit activity
    Python 42 MIT 10 0 0 Updated Dec 24, 2025
  • Himito Public
    broadinstitute/Himito’s past year of commit activity
    WDL 5 MIT 0 0 0 Updated Dec 24, 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 6 1 10 2 Updated Dec 24, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,896 622 1,271 (8 issues need help) 143 Updated Dec 24, 2025
  • genomeshader Public

    Visualization of biobank-scale genomic datasets.

    broadinstitute/genomeshader’s past year of commit activity
    HTML 3 BSD-3-Clause 0 7 (2 issues need help) 2 Updated Dec 23, 2025
  • gnomad-constraint Public
    broadinstitute/gnomad-constraint’s past year of commit activity
    Python 5 BSD-3-Clause 0 0 1 Updated Dec 23, 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 23, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 26 BSD-3-Clause 4 0 4 Updated Dec 23, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 199 BSD-3-Clause 76 94 26 Updated Dec 23, 2025
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