Common data model proposal for biomedical research intended to facilitate and encourage data sharing and reuse

Microsoft Genomics implementation of the Broad Institute's Cromwell workflow engine on Azure

Given the output directory of a QC pipeline and a threshold config file, parse out the desired metrics and evalute them against the thresholds.

Comprehensive alignment, whole-genome coverage, and capture coverage statistics.

Open workflow definitions for genomic analysis from MGI at WUSM.

a place for GA4GH-related wiki pages

Strelka2 germline and somatic small variant caller

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

Examples for the Google Genomics Pipelines API.

A WDL, CWL and Python API supporting easy-to-use workflow engine. It is scalable, efficient and cross-platform (Linux/macOS).

Apache Superset is a Data Visualization and Data Exploration Platform

Specifications of SAM/BAM and related high-throughput sequencing file formats

An open source platform for managing and analyzing biomedical big data

DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools

Tools for processing and analyzing structural variants.

The Genome Modeling System installer

Compliance test suite for the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

library/utility for creating process streams on Linux (pipes, fanout).

Models and APIs for Genomic data. RETIRED 2018-01-24

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

[Historical] Reproducible Analyses for Bioinformatics

Core modules used by the GMS

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file form…

Unofficial repo for software vendoring or packaging purposes