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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 1.7k 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
  • accessibility_peak_gene_predictor Public
    broadinstitute/accessibility_peak_gene_predictor’s past year of commit activity
    Python 0 0 0 0 Updated Sep 20, 2024
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 176 AGPL-3.0 87 56 5 Updated Sep 20, 2024
  • viral-phylo Public

    viral-ngs: phylogenetics, annotation, intrahost variants

    broadinstitute/viral-phylo’s past year of commit activity
    Python 1 0 8 2 Updated Sep 20, 2024
  • viral-assemble Public

    viral-ngs: genome assembly and scaffolding

    broadinstitute/viral-assemble’s past year of commit activity
    Python 7 2 2 1 Updated Sep 20, 2024
  • viral-core Public

    viral-ngs: read QC, barcode metrics, spike-in metrics, Illumina metrics and demux

    broadinstitute/viral-core’s past year of commit activity
    Python 3 0 9 1 Updated Sep 20, 2024
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 52 28 22 16 Updated Sep 20, 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 72 25 Updated Sep 19, 2024
  • Drop-seq Public

    Java tools for analyzing Drop-seq data

    broadinstitute/Drop-seq’s past year of commit activity
    Java 119 MIT 34 19 0 Updated Sep 19, 2024
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 5 0 0 12 Updated Sep 19, 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 28 (1 issue needs help) 5 Updated Sep 19, 2024
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