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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 587

  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 969 370

  3. cromwell cromwell Public

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

    Scala 988 357

Repositories

Showing 10 of 1294 repositories
  • 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 62 BSD-3-Clause 26 0 4 Updated Sep 19, 2024
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 7 BSD-3-Clause 5 0 9 Updated Sep 19, 2024
  • ops-terra-utils Public
    broadinstitute/ops-terra-utils’s past year of commit activity
    Python 1 0 0 2 Updated Sep 19, 2024
  • accessibility_peak_gene_predictor Public
    broadinstitute/accessibility_peak_gene_predictor’s past year of commit activity
    Python 0 0 0 0 Updated Sep 19, 2024
  • datarepo-helm Public

    A helm repo for Broad Data Science Platforms helm charts

    broadinstitute/datarepo-helm’s past year of commit activity
    Mustache 5 1 0 5 Updated Sep 19, 2024
  • datarepo-helm-definitions Public

    Helm deployment specific values and definitions for Dev, Integration and Prod

    broadinstitute/datarepo-helm-definitions’s past year of commit activity
    Shell 3 1 0 10 Updated Sep 19, 2024
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 169 BSD-3-Clause 70 73 27 Updated Sep 19, 2024
  • thurloe Public

    A simple service to store arbitrary key/value pairs

    broadinstitute/thurloe’s past year of commit activity
    Scala 3 BSD-3-Clause 0 0 40 Updated Sep 19, 2024
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 52 28 22 18 Updated Sep 19, 2024
  • viral-assemble Public

    viral-ngs: genome assembly and scaffolding

    broadinstitute/viral-assemble’s past year of commit activity
    Python 7 2 2 0 Updated Sep 19, 2024
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