Open Access Research

Fastbreak: a tool for analysis and visualization of structural variations in genomic data

Ryan Bressler1, Jake Lin1, Andrea Eakin1, Thomas Robinson1, Richard Kreisberg1, Hector Rovira1, Theo Knijnenburg1,2, John Boyle1 and Ilya Shmulevich1*

Author Affiliations

1 Institute for System Biology, 401 Terry Avenue North, Seattle, WA, 98109-5234, USA

2 Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066CX, The Netherlands

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EURASIP Journal on Bioinformatics and Systems Biology 2012, 2012:15 doi:10.1186/1687-4153-2012-15

Published: 9 October 2012

Abstract

Genomic studies are now being undertaken on thousands of samples requiring new computational tools that can rapidly analyze data to identify clinically important features. Inferring structural variations in cancer genomes from mate-paired reads is a combinatorially difficult problem. We introduce Fastbreak, a fast and scalable toolkit that enables the analysis and visualization of large amounts of data from projects such as The Cancer Genome Atlas.

Keywords:
Cancer genomics; Structural variation; Translocation