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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 602

  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 374

  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 363

Repositories

Showing 10 of 1377 repositories
  • seqr-loading-pipelines Public

    hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

    broadinstitute/seqr-loading-pipelines’s past year of commit activity
    Python 23 MIT 20 28 5 Updated May 7, 2025
  • cromwell Public

    Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

    broadinstitute/cromwell’s past year of commit activity
    Scala 1,016 BSD-3-Clause 363 746 52 Updated May 7, 2025
  • idmp-fungal-pipelines Public
    broadinstitute/idmp-fungal-pipelines’s past year of commit activity
    WDL 0 GPL-3.0 0 0 1 Updated May 7, 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 May 7, 2025
  • seqr-helm Public

    Helm charts for the seqr project

    broadinstitute/seqr-helm’s past year of commit activity
    Python 3 BSD-3-Clause 2 1 0 Updated May 7, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 187 BSD-3-Clause 75 83 24 Updated May 7, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,800 602 1,246 (8 issues need help) 137 Updated May 7, 2025
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 212 BSD-3-Clause 104 5 15 Updated May 6, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 25 BSD-3-Clause 4 0 6 Updated May 6, 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 May 6, 2025
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