Genomes-in-the-cloud is a genomic analysis pipeline project developed by the Broad Institute.
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Readme

The genomes-in-the-cloud Docker image contains a collection of software packages used in Broad production pipelines to perform genomic analyses.

IMPORTANT: This Docker image is provided to the public to facilitate reproducibility and standardization of analyses. Users are responsible for complying with the licensing terms of all included packages regarding use and redistribution; see summary table below.

PackageProject URLLicense Type
Picardhttp://broadinstitute.github.io/picard/MIT
BWA memhttp://bio-bwa.sourceforge.net/GPLv3/MIT
GATKhttps://www.broadinstitute.org/gatk/See below
Samtoolshttp://www.htslib.org/MIT/Expat
VerifyBamIDhttp://genome.sph.umich.edu/wiki/VerifyBamIDMIT
Python 3https://www.python.org/PSF/GPL-compat
Rhttps://www.r-project.org/GPLv2/GPLv3
ggplot 2http://ggplot2.org/GPLv2
Java 8 Runtimehttp://openjdk.java.net/projects/jdk8/GPLv2

GATK licensing

The GATK is licensed by the Broad Institute and is made available for free to academic users for non-commercial use only pursuant to the licensing terms below, and to other authorized licensees pursuant to the terms of their respective licenses, in each case for use within this pipeline only. The full text of the academic license for non-commercial use of GATK is available here. For commercial licensing information, please email softwarelicensing@broadinstitute.org.