OSA (Omicsoft Sequence Aligner), a super-fast and accurate alignment tool for RNA-Seq data. Benchmarked with existing methods, OSA improves mapping 
speed 4-10 folds with better sensitivity and less false positives. 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.
This latest version will take all the read that does not align perfectly on the transcriptome to the genome. It also optimizes the steps to align reads with novel junctions or having a potential exon junction close to the end. Overall, OSA v1.7.3 aligns 1-2% of more reads acurrately to the genome compared to the OSA v1.5.1. The alignment speed is a little slower compared with the previous version, especially for alignment with gene model at higher error rate. However, it is still much faster than other tools we have benchmarked with.
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.
Reference:
Hu J, Ge H, Newman M, Liu K. OSA: a fast and accurate alignment tool for RNA-Seq. Bioinformatics. 2012 Jul 15;28(14):1933-4. Epub 2012 May 15. PubMed PMID: 22592379.
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