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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 594

  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 984 369

  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 1322 repositories
  • pav-wdl Public Forked from wharvey31/pav-wdl

    Workspace for WDL implementation of PAV

    broadinstitute/pav-wdl’s past year of commit activity
    WDL 0 3 0 0 Updated Nov 29, 2024
  • pyqtl Public

    Collection of analysis tools for quantitative trait loci

    broadinstitute/pyqtl’s past year of commit activity
    Python 41 BSD-3-Clause 8 0 2 Updated Nov 29, 2024
  • delphy Public

    Fast, scalable, accurate and accessible Bayesian phylogenetics

    broadinstitute/delphy’s past year of commit activity
    C++ 27 3 0 0 Updated Nov 29, 2024
  • 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 2 Updated Nov 29, 2024
  • 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 30 (1 issue needs help) 1 Updated Nov 29, 2024
  • str-analysis Public

    Scripts and utilities related to analyzing short tandem repeats (STRs).

    broadinstitute/str-analysis’s past year of commit activity
    Python 32 MIT 8 1 0 Updated Nov 29, 2024
  • heimdall Public
    broadinstitute/heimdall’s past year of commit activity
    Shell 0 0 0 0 Updated Nov 29, 2024
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 8 BSD-3-Clause 5 0 8 Updated Nov 29, 2024
  • hidive Public
    broadinstitute/hidive’s past year of commit activity
    Rust 0 BSD-3-Clause 0 3 2 Updated Nov 28, 2024
  • gnomad_methods Public

    Hail helper functions for the gnomAD project and Translational Genomics Group

    broadinstitute/gnomad_methods’s past year of commit activity
    Python 89 MIT 29 10 10 Updated Nov 28, 2024
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