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.