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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 1.7k 596

  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 992 371

  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 360

Repositories

Showing 10 of 1333 repositories
  • Drop-seq Public

    Java tools for analyzing Drop-seq data

    broadinstitute/Drop-seq’s past year of commit activity
    Java 123 MIT 35 22 2 Updated Jan 14, 2025
  • monorepo Public

    Compendium of tools for the Imaging Platform

    broadinstitute/monorepo’s past year of commit activity
    Python 9 BSD-3-Clause 1 12 1 Updated Jan 14, 2025
  • 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 22 MIT 20 25 2 Updated Jan 14, 2025
  • broad-epi-repeats-analysis Public

    Workflow to quantify transposable elements expression.

    broadinstitute/broad-epi-repeats-analysis’s past year of commit activity
    WDL 0 0 0 0 Updated Jan 14, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,745 596 1,231 (8 issues need help) 136 Updated Jan 14, 2025
  • seqr-helm Public

    Helm charts for the seqr project

    broadinstitute/seqr-helm’s past year of commit activity
    Python 1 BSD-3-Clause 1 0 1 Updated Jan 14, 2025
  • exome-results-browsers Public

    Results browsers for case-control studies of psychiatric diseases done at the Broad Institute

    broadinstitute/exome-results-browsers’s past year of commit activity
    JavaScript 11 BSD-3-Clause 4 6 3 Updated Jan 14, 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 1,007 BSD-3-Clause 360 745 50 Updated Jan 14, 2025
  • kinnex-preliminary-processing Public
    broadinstitute/kinnex-preliminary-processing’s past year of commit activity
    Python 0 0 0 0 Updated Jan 14, 2025
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 207 BSD-3-Clause 100 7 18 Updated Jan 14, 2025
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