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Big Data Genomics: ADAM

ADAM: Data Alignment/Map

ADAM provides both an application programming interface (API) and a command line interface (CLI) for manipulating genomic data on a computing cluster. ADAM operates on data stored inside of Parquet with the bdg-formats schemas, using Apache Spark, and provides scalable performance on clusters larger than 100 machines.

ADAM is on Github. Quick start guides are available for running ADAM on EC2, and for building ADAM for specific CDH releases.

Releases

The latest available release of ADAM is 0.6.1. ADAM is available for projects using Maven or SBT through the Sonatype OSS repository.

Support

For support using ADAM, please contact the ADAM developer mailing list. Additionally, we track issues and feature enhancement requests through our Github issue tracker.

Citing

ADAM has been described in a UC Berkeley EECS technical report. The Bibtex for this reference is:

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@techreport{Massie:EECS-2013-207,
    Author = {Massie, Matt and Nothaft, Frank and Hartl, Christopher and Kozanitis, Christos and Schumacher, André and Joseph, Anthony D. and Patterson, David A.},
    Title = {ADAM: Genomics Formats and Processing Patterns for Cloud Scale Computing},
    Institution = {EECS Department, University of California, Berkeley},
    Year = {2013},
    Month = {Dec},
    URL = {http://www.eecs.berkeley.edu/Pubs/TechRpts/2013/EECS-2013-207.html},
    Number = {UCB/EECS-2013-207}
}

Licensing

ADAM is available under the Apache 2 open source software (OSS) license. This OSS license is non-viral, and places no restrictions on users who would like to use or modify the software.

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