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    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•0•6•Updated Nov 8, 2024Nov 8, 2024

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •20•22•31•2•Updated Nov 8, 2024Nov 8, 2024

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•0•4•Updated Nov 8, 2024Nov 8, 2024

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•42•3•38•Updated Nov 8, 2024Nov 8, 2024

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •590•1.7k•1.2k•140•Updated Nov 8, 2024Nov 8, 2024

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•20•Updated Nov 8, 2024Nov 8, 2024

    • data-registry

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•8•Updated Nov 8, 2024Nov 8, 2024

    • data-registry-api

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Nov 8, 2024Nov 8, 2024

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •44•81•160•15•Updated Nov 8, 2024Nov 8, 2024

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•4•Updated Nov 8, 2024Nov 8, 2024

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •96•202•8•23•Updated Nov 8, 2024Nov 8, 2024

    • ml4h

      Public
      Python
      •
      Other
      •23•122•30•20•Updated Nov 8, 2024Nov 8, 2024

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•176•54•4•Updated Nov 8, 2024Nov 8, 2024

    • ops-terra-utils

      Public
      Python
      •0•3•0•2•Updated Nov 8, 2024Nov 8, 2024

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•3•Updated Nov 8, 2024Nov 8, 2024

    • tgg_methods

      Public
      Repo for miscellaneous methods developed by the methods group that don't fit anywhere else
      Python
      •
      MIT License
      •0•4•5•4•Updated Nov 8, 2024Nov 8, 2024

    • epi-SHARE-seq-pipeline

      Public
      Epigenomics Program pipeline to analyze SHARE-seq data.
      WDL
      •
      MIT License
      •3•17•28•1•Updated Nov 8, 2024Nov 8, 2024

    • malaria

      Public
      WDL
      •
      MIT License
      •0•1•2•0•Updated Nov 8, 2024Nov 8, 2024

    • stp_space_ranger

      Public
      WDL
      •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • 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.
      WDL
      •0•1•21•2•Updated Nov 8, 2024Nov 8, 2024

    • broad-epi-workflows-collection

      Public
      This repo contains WDL workflows written by the Epigenomics program.
      WDL
      •
      MIT License
      •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • warp-tools

      Public
      This repository contains all containers that WARP uses.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•8•1•10•Updated Nov 8, 2024Nov 8, 2024

    • firecloud-orchestration

      Public
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•31•0•1•Updated Nov 8, 2024Nov 8, 2024

    • long-read-pipelines

      Public
      Long read production pipelines
      pipelineswdlvariant-callingde-novo-assemblylong-reads
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •25•141•95•26•Updated Nov 8, 2024Nov 8, 2024

    • funpipe

      Public
      A python3 library for building best practice fungal genomic analysis pipeline
      geneticspython-librarypython3bioinformatics-pipelinefungalinfectious-diseasegenomics
      HTML
      •
      MIT License
      •4•6•35•2•Updated Nov 8, 2024Nov 8, 2024

    • heimdall

      Public
      Shell
      •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • SpliceAI-lookup-dev

      Public
      dev UIs for spliceai-lookup.broadinstitute.org
      HTML
      •
      MIT License
      •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • viral-core

      Public
      viral-ngs: read QC, barcode metrics, spike-in metrics, Illumina metrics and demux
      Python
      •
      Other
      •0•3•9•1•Updated Nov 8, 2024Nov 8, 2024

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •72•171•73•22•Updated Nov 8, 2024Nov 8, 2024

    • lembic

      Public
      Distilling some data for CFDE
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024