Item

Abstract

Short mRNA sequences produced by RNA-Seq enhance transcriptome analysis and promise great opportunities for the discovery of new genes and the identification of alternative transcripts. However, the sheer amount of high throughput sequencing data requires efficient methods for accurate spliced alignments of reads against the reference genome, which is further challenged by size and quality of the sequence reads. We present an original RNA-Seq read mapper, called PALMapper, that combines a faster extension of the high accurate alignment method QPALMA with the fast short read aligner GenomeMapper. PALMapper quickly carries out an initial read mapping which then guides a Banded Semi-Global alignment algorithm that allows for long gaps corresponding to introns. PALMapper drastically improves the speed of QPALMA (around 50 times faster) and still computes both spliced and unspliced alignments at high accuracy by taking advantage of base quality information and computational splice site predictions. Moreover, PALMapper is under active development and offers a growing pool of features such as polyA trimming or non-canonical splice site support, which can improve again alignment accuracy for specific downstream studies. Finally, PALMapper does not rely on any annotation but is able to remap reads against an inferred splice junction database. This strategy applied on simulated data from C. elegans increases the number of correct spliced alignments from 89% to 92% while the incorrect alignments decrease by 27%. On the same dataset, we show that PALMapper outperfoms GSNAP and TopHat, two other widely used alignment tools.