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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
  • depmap-omics-wgs Public
    broadinstitute/depmap-omics-wgs’s past year of commit activity
    Python 0 0 3 0 Updated May 8, 2025
  • stp_segmentation_wdl Public
    broadinstitute/stp_segmentation_wdl’s past year of commit activity
    WDL 0 0 0 0 Updated May 8, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 5 0 1 17 Updated May 7, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 187 AGPL-3.0 90 48 2 Updated May 7, 2025
  • 2025_Grigoryan_Proteomics Public

    Repo for analysis of the Nomic Bio proteomics pilot data, collected as part of the OASIS Consortium

    broadinstitute/2025_Grigoryan_Proteomics’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 2 6 0 Updated May 7, 2025
  • cromwhelm Public

    Tentative first steps into the world of helm charts

    broadinstitute/cromwhelm’s past year of commit activity
    Smarty 2 2 0 2 Updated May 7, 2025
  • regional_missense_constraint Public

    Code to calculate regional missense constraint

    broadinstitute/regional_missense_constraint’s past year of commit activity
    Python 13 BSD-3-Clause 1 1 1 Updated May 7, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 1 1 0 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 363 747 51 Updated May 7, 2025
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 8 BSD-2-Clause 1 0 10 Updated May 7, 2025
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