RASER: reads aligner for SNPs and editing sites of RNA.

ABSTRACT:

Motivation

Accurate identification of genetic variants such as single-nucleotide polymorphisms (SNPs) or RNA editing sites from RNA-Seq reads is important, yet challenging, because it necessitates a very low false-positive rate in read mapping. Although many read aligners are available, no single aligner was specifically developed or tested as an effective tool for SNP and RNA editing prediction.

Results

We present RASER, an accurate read aligner with novel mapping schemes and index tree structure that aims to reduce false-positive mappings due to existence of highly similar regions. We demonstrate that RASER shows the best mapping accuracy compared with other popular algorithms and highest sensitivity in identifying multiply mapped reads. As a result, RASER displays superb

SUBMITTER: Ahn J 

PROVIDER: S-EPMC4692970 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature