OSA: a fast and accurate alignment tool for RNA-Seq
J Hu, H Ge, M Newman, K Liu - Bioinformatics, 2012 - academic.oup.com
J Hu, H Ge, M Newman, K Liu
Bioinformatics, 2012•academic.oup.comAccurately 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 …
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 …
Abstract
Summary: 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.
Contact: john.hu@omicsoft.com; jhu7@ncsu.edu; jack.liu@omicsoft.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Oxford University Press