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adam

A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

adam-fs-benchmarks

adam-queries

Small queries to run on ADAM for GDA.

adam-regression

Regression testing setup for ADAM.

adam-snpeff

SnpEff on Spark via ADAM pipe APIs

ananas

avocado

A Variant Caller, Distributed

bdg-formats

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

bdg-recipes

Recipes using BDG projects. Apache 2 licensed.

bdg-services

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

bdg-utils

General (non-omics) code used across BDG products. Apache 2 licensed.

bigdata_2015

bigdatagenomics.github.io

Web Site for the Big Data Genomics Group

bits

Firebox Benchmarks

blog

cannoli

A little, Apache 2 licensed pipe.

cannoli-1

Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools. Apache 2 licensed.

cgcloud

Image and VM management for Jenkins, Spark and Mesos clusters in EC2

cgl-docker-lib

cloud-scale-bwamem

conductor

Efficient, distributed downloads of large files from S3 to HDFS using Spark.

copier

Apache Spark-based tool for downloading a list of URLs. Apache 2 licensed.

corretto

Read error correction utilities.

deca

Distributed exome CNV analyzer. Apache 2 licensed.

docker-images

Miscellaneous Docker images.

docs

My writings.

eggo

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

fig

A tool for Finding Interesting variants that modify regulatory Grammar.

fnothaft.github.io

Personal website.

gatk

Official code repository for GATK versions 4 and up