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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 597

  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 993 371

  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 1334 repositories
  • lrma-aou1-panel-creation Public

    Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.

    broadinstitute/lrma-aou1-panel-creation’s past year of commit activity
    WDL 1 0 22 2 Updated Jan 25, 2025
  • pyqtl Public

    Collection of analysis tools for quantitative trait loci

    broadinstitute/pyqtl’s past year of commit activity
    Python 48 BSD-3-Clause 8 0 2 Updated Jan 25, 2025
  • PTA_Analysis Public
    broadinstitute/PTA_Analysis’s past year of commit activity
    WDL 0 0 0 0 Updated Jan 25, 2025
  • ygramul Public

    Hierarchical knowledge graph for PIGEAN results

    broadinstitute/ygramul’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 0 Updated Jan 25, 2025
  • backstage Public

    Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)

    broadinstitute/backstage’s past year of commit activity
    TypeScript 2 0 5 5 Updated Jan 25, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 4 0 1 10 Updated Jan 25, 2025
  • dcc_pigean_flask Public

    Flask server for the Pigean method

    broadinstitute/dcc_pigean_flask’s past year of commit activity
    Python 0 1 2 0 Updated Jan 25, 2025
  • imaging-platform-pipelines Public

    Cell Painting and other pipelines from the Imaging Platform

    broadinstitute/imaging-platform-pipelines’s past year of commit activity
    15 13 2 2 Updated Jan 25, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 176 BSD-3-Clause 72 74 23 Updated Jan 24, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,753 597 1,232 (8 issues need help) 137 Updated Jan 24, 2025
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