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Bioinformatics. 2012 Jul 15;28(14):1933-4. doi: 10.1093/bioinformatics/bts294. Epub 2012 May 15.

OSA: a fast and accurate alignment tool for RNA-Seq.

Author information

1
Division of Bioinformatics, Omicsoft Inc., 164 Quade Drive, Cary, NC 27513, USA. john.hu@omicsoft.com

Abstract

Accurately mapping RNA-Seq reads to the reference genome is a critical step for performing downstream analysis such as transcript assembly, isoform detection and quantification. Many tools have been developed; however, given the huge size of the next generation sequencing datasets and the complexity of the transcriptome, RNA-Seq read mapping remains a challenge with the ever-increasing amount of data. We develop Omicsoft sequence aligner (OSA), a fast and accurate alignment tool for RNA-Seq data. Benchmarked with existing methods, OSA improves mapping speed 4-10-fold with better sensitivity and less false positives.

AVAILABILITY:

OSA can be downloaded from http://omicsoft.com/osa. It is free to academic users. OSA has been tested extensively on Linux, Mac OS X and Windows platforms.

PMID:
22592379
DOI:
10.1093/bioinformatics/bts294
[Indexed for MEDLINE]

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