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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 1.8k 603

  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 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 360

Repositories

Showing 10 of 1355 repositories
  • warp-tools Public

    This repository contains all containers that WARP uses.

    broadinstitute/warp-tools’s past year of commit activity
    Python 9 BSD-3-Clause 2 1 11 Updated Mar 24, 2025
  • viral-references Public

    Reference tables for viral genomics

    broadinstitute/viral-references’s past year of commit activity
    4 BSD-2-Clause 2 0 0 Updated Mar 24, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 26 BSD-3-Clause 4 0 11 Updated Mar 24, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 185 AGPL-3.0 89 49 4 Updated Mar 24, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 1 1 0 Updated Mar 24, 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 23 MIT 20 21 3 Updated Mar 24, 2025
  • depmap_omics Public

    What you need to process the Quarterly DepMap-Omics releases from Terra

    broadinstitute/depmap_omics’s past year of commit activity
    HTML 114 22 3 5 Updated Mar 24, 2025
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 9 BSD-3-Clause 5 0 18 Updated Mar 24, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,784 603 1,239 (8 issues need help) 133 Updated Mar 24, 2025
  • single_cell_portal_core Public

    Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

    broadinstitute/single_cell_portal_core’s past year of commit activity
    Ruby 67 BSD-3-Clause 26 0 3 Updated Mar 24, 2025
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