Broad Institute

Repositories

• covid19-testing

  COVID-19 Diagnostic Processing Dashboard
  HTML MIT 3 18 2 0 Updated Jul 21, 2021

• ML_for_slideseq

  Fedor / Luca project to develop ML tool which interpretes slideseq data
  Jupyter Notebook 0 0 6 2 Updated Jul 21, 2021

• cromwell

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

  docker application workflow cloud bioinformatics scala executor
  Scala 242 711 696 68 Updated Jul 21, 2021

• sc2-rmd
  Python BSD-2-Clause 0 0 0 0 Updated Jul 21, 2021

• lunaris

  Lunaris reads and munges data from block-gzipped, location-sorted, tabix-indexed files on Google Cloud.
  Scala BSD-3-Clause 1 1 1 1 Updated Jul 21, 2021

• depmap_omics

  What you need to process the Quarterly DepMap-Omics releases from Terra

  data-science cancer-genomics cloud-computing depmap
  HTML 6 26 1 2 Updated Jul 21, 2021

• rawls

  Rawls service for DSDE
  Scala 2 13 0 15 Updated Jul 20, 2021

• gatk-sv
  wdl BSD-3-Clause 20 55 43 4 Updated Jul 20, 2021

• gatk

  Official code repository for GATK versions 4 and up

  science bioinformatics spark genomics genome ngs sequencing
  Java 424 1,074 996 (8 issues need help) 93 Updated Jul 20, 2021

• selene

  BGZ/TBI Reader
  Rust BSD-3-Clause 0 0 0 0 Updated Jul 20, 2021

• ddp-study-server

  Pepper Study Server
  Java BSD-3-Clause 0 4 0 19 Updated Jul 20, 2021

• long-read-pipelines

  Long read production pipelines

  pipelines wdl variant-calling de-novo-assembly long-reads
  Jupyter Notebook BSD-3-Clause 5 46 37 (5 issues need help) 6 Updated Jul 20, 2021

• monster-deploy

  Infrastructure-as-code for Monster team's "core" environments
  HCL BSD-3-Clause 0 2 0 2 Updated Jul 20, 2021

• martha

  Google Cloud Function for Blue Box/GUID resolution
  JavaScript BSD-3-Clause 3 2 3 7 Updated Jul 20, 2021

• ddp-study-manager

  Pepper Study Manager
  Java BSD-3-Clause 1 2 0 11 Updated Jul 20, 2021

• gnomad_methods

  Hail helper functions for the gnomAD project and Translational Genomics Group

  genomics genomes exomes hail
  Python MIT 17 35 61 3 Updated Jul 20, 2021

• gnomad-readviz

  scripts that precompute minibams and other files necessary for the readviz feature of https://gnomad.broadinstitute.org
  Python MIT 0 1 0 0 Updated Jul 20, 2021

• tgg-terraform-modules
  HCL 0 0 0 0 Updated Jul 20, 2021

• bits-ap-modules
  HCL 0 0 5 0 Updated Jul 20, 2021

• gcp-dm-templates

  Templates and code for creating FireCloud GCP projects with Deployment Manager
  Python 0 0 1 2 Updated Jul 20, 2021

• warp

  WDL Analysis Research Pipelines
  wdl BSD-3-Clause 22 52 8 14 Updated Jul 20, 2021

• hail-elasticsearch-pipelines

  hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
  Python MIT 8 14 26 4 Updated Jul 20, 2021

• palantir-workflows

  Utility workflows for the DSP palantir team
  wdl BSD-3-Clause 1 7 3 4 Updated Jul 20, 2021

• firecloud-orchestration
  Scala BSD-3-Clause 4 23 0 6 Updated Jul 20, 2021

• ddp-angular

  Angular code for participant-facing pepper studies
  TypeScript 1 1 0 20 Updated Jul 20, 2021

• wfl

  WorkFlow Launcher (née Zero)
  Clojure BSD-3-Clause 0 8 0 7 Updated Jul 20, 2021

• gnomad-browser

  javascript genomics gnomad
  JavaScript MIT 20 50 97 1 Updated Jul 20, 2021

• single_cell_portal_core

  Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

  rna-seq-analysis single-cell-genomics human-cell-atlas
  Ruby BSD-3-Clause 19 40 0 2 Updated Jul 20, 2021

• ddp-study-manager-ui

  Pepper Study Manager UI
  TypeScript BSD-3-Clause 0 1 0 3 Updated Jul 20, 2021

• terra-helm

  A helm repo for Terra from Broad Data Science Platforms Group
  Smarty BSD-3-Clause 1 7 0 5 Updated Jul 20, 2021