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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 1.8k 597

  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 993 372

  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 359

Repositories

Showing 10 of 1334 repositories
  • gtex-pipeline Public

    GTEx & TOPMed data production and analysis pipelines

    broadinstitute/gtex-pipeline’s past year of commit activity
    Python 355 BSD-3-Clause 177 10 3 Updated Jan 27, 2025
  • bits-appengine Public

    BITS AppEngine Python Package

    broadinstitute/bits-appengine’s past year of commit activity
    Python 0 0 0 1 Updated Jan 27, 2025
  • sherlock Public

    DSP DevOps's deployment source-of-truth service

    broadinstitute/sherlock’s past year of commit activity
    Go 1 BSD-3-Clause 0 0 10 Updated Jan 27, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 1 0 0 Updated Jan 26, 2025
  • mitograph Public
    broadinstitute/mitograph’s past year of commit activity
    Rust 0 0 0 0 Updated Jan 26, 2025
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 9 BSD-3-Clause 5 0 7 Updated Jan 26, 2025
  • PTA_Analysis Public
    broadinstitute/PTA_Analysis’s past year of commit activity
    WDL 0 0 0 0 Updated Jan 26, 2025
  • lrma-aou1-panel-creation Public

    Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.

    broadinstitute/lrma-aou1-panel-creation’s past year of commit activity
    WDL 1 0 22 2 Updated Jan 25, 2025
  • pyqtl Public

    Collection of analysis tools for quantitative trait loci

    broadinstitute/pyqtl’s past year of commit activity
    Python 48 BSD-3-Clause 8 0 2 Updated Jan 25, 2025
  • ygramul Public

    Hierarchical knowledge graph for PIGEAN results

    broadinstitute/ygramul’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 0 Updated Jan 25, 2025
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