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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 1.6k 579

  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 952 366

  3. cromwell cromwell Public

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

    Scala 970 353

Repositories

Showing 10 of 1260 repositories
  • ABC-Enhancer-Gene-Prediction Public

    Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

    broadinstitute/ABC-Enhancer-Gene-Prediction’s past year of commit activity
    Python 189 MIT 56 12 0 Updated Jun 29, 2024
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 4 BSD-3-Clause 5 0 7 Updated Jun 29, 2024
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 160 BSD-3-Clause 71 68 19 Updated Jun 29, 2024
  • datarepo-helm Public

    A helm repo for Broad Data Science Platforms helm charts

    broadinstitute/datarepo-helm’s past year of commit activity
    Mustache 4 1 0 5 Updated Jun 29, 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 Jun 29, 2024
  • gene-trends Public

    Explore gene trends over time - BroadHacks 2024

    broadinstitute/gene-trends’s past year of commit activity
    Jupyter Notebook 2 BSD-3-Clause 0 0 0 Updated Jun 28, 2024
  • sherlock Public

    DSP DevOps's deployment source-of-truth service

    broadinstitute/sherlock’s past year of commit activity
    Go 1 BSD-3-Clause 0 0 4 Updated Jun 28, 2024
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 193 BSD-3-Clause 89 7 26 Updated Jun 28, 2024
  • warp-tools Public

    This repository contains all containers that WARP uses.

    broadinstitute/warp-tools’s past year of commit activity
    Python 9 BSD-3-Clause 2 1 9 Updated Jun 28, 2024
  • cromwell-develop Public

    Repository for Broad specific cromwell **configs**. For the cromwell software, see https://github.com/broadinstitute/cromwell

    broadinstitute/cromwell-develop’s past year of commit activity
    Shell 1 0 0 1 Updated Jun 28, 2024
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