BAsplice: Bi-direction alignment for detecting splice junctions

Abstract

RNA-Seq is a revolutionary whole transcriptome shotgun sequencing technology performed by high-throughput sequencers, which provide more comprehensive information on differential expression of genes and benefit on novel splice variants identification. RNA-Seq reads is so short that it's a great challenge on mapping reads back to the reference effectively, especially when they span two or more exons. To improve the mapping efficiency, we introduce here a bi-direction alignment tool - BAsplice, which use RNA-Seq data to detect splice junctions without any additional information. Compare with another splice junction mapping software, SOAPsplice, BAsplice performs better in call rate and running time, but a little worse in accuracy. BAsplice is a free open-source software written in C language. It is available at https://github.com/vlcc/basplice.