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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 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 991 371

  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 359

Repositories

Showing 10 of 1331 repositories
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 207 BSD-3-Clause 99 7 25 Updated Jan 8, 2025
  • ops-terra-utils Public
    broadinstitute/ops-terra-utils’s past year of commit activity
    Python 3 0 0 1 Updated Jan 8, 2025
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 9 BSD-3-Clause 5 0 10 Updated Jan 8, 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 63 BSD-3-Clause 26 0 1 Updated Jan 8, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 179 AGPL-3.0 89 48 6 Updated Jan 8, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 175 BSD-3-Clause 71 74 27 Updated Jan 8, 2025
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 7 BSD-2-Clause 1 0 6 Updated Jan 8, 2025
  • bibt-slack Public

    Broad Institute BITS Blue Team repository for bibt-slack PyPI library.

    broadinstitute/bibt-slack’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jan 8, 2025
  • bibt-sentinelone Public

    Broad Institute BITS Blue Team repository for bibt-sentinelone PyPI library.

    broadinstitute/bibt-sentinelone’s past year of commit activity
    Makefile 0 MIT 0 0 0 Updated Jan 8, 2025
  • bibt-qualys Public

    Broad Institute BITS Blue Team repository for bibt-qualys PyPI library.

    broadinstitute/bibt-qualys’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jan 8, 2025
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