Big Data Genomics

adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

mango

A scalable genome browser. Apache 2 licensed.

avocado

A Variant Caller, Distributed. Apache 2 licensed.

bdg-formats

Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.

cannoli

Distributed execution of bioinformatics tools on Apache Spark. Apache 2 licensed.

eggo

Ready-to-go Parquet-formatted public 'omics datasets

rice

An RNA pipeline built on top of ADAM. Apache 2 licensed.

utils

General utility code used across BDG products. Apache 2 licensed.

awesome-adam

Awesome list of applications that extend Big Data Genomics ADAM. CC0 licensed.

bigdatagenomics.github.io

Web Site for the Big Data Genomics Group

gnocchi

bdg-services

Utility classes for wrapping services or other interfaces around a Spark/ADAM cluster. Apache 2 licensed.

lime

Distributed Set Theory for Genomics

workflows

Toil workflows for bigdatagenomics tools. Apache 2 licensed.

recipes

Recipes using BDG projects. Apache 2 licensed.

deca

Distributed exome CNV analyzer. Apache 2 licensed.

mango-notebook

Notebook tools for Big Data Genomics. Apache 2 licensed.

PacMin

Assembler for PacBio reads. Apache 2 licensed.

quinine

A refreshing treatment for all quality control ailments. Apache 2 licensed.

jenkins-docker

toil-wdl-api

Exemplar API that mediates Toil with a WDL front-end and workflow tracking.

convert

Conversions to and from Big Data Genomics Avro Formats. Apache 2 licensed.

corretto

Read error correction utilities.