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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 984 368

  3. cromwell cromwell Public

    Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

    Scala 998 361

Repositories

Showing 10 of 1319 repositories
  • sam Public

    workbench identity and access management

    broadinstitute/sam’s past year of commit activity
    Scala 42 BSD-3-Clause 12 3 29 Updated Nov 22, 2024
  • orsp-pub Public

    Public ORSP Compliance Portal

    broadinstitute/orsp-pub’s past year of commit activity
    JavaScript 3 BSD-3-Clause 0 0 25 Updated Nov 22, 2024
  • juniper0 Public

    Preliminary Version of JUNIPER: Large-Scale Outbreak Reconstruction

    broadinstitute/juniper0’s past year of commit activity
    R 2 MIT 0 0 0 Updated Nov 22, 2024
  • heimdall Public
    broadinstitute/heimdall’s past year of commit activity
    Shell 0 0 0 0 Updated Nov 22, 2024
  • data-registry Public
    broadinstitute/data-registry’s past year of commit activity
    Vue 0 BSD-3-Clause 1 0 9 Updated Nov 22, 2024
  • data-registry-api Public
    broadinstitute/data-registry-api’s past year of commit activity
    Python 1 BSD-3-Clause 1 0 0 Updated Nov 22, 2024
  • molecular-data-provider Public

    Molecular Data Provider

    broadinstitute/molecular-data-provider’s past year of commit activity
    Python 11 MIT 8 3 5 Updated Nov 22, 2024
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 62 27 23 16 Updated Nov 22, 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 31 (1 issue needs help) 5 Updated Nov 21, 2024
  • 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 Nov 21, 2024
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