RASER: reads aligner for SNPs and editing sites of RNA

Bioinformatics
Jaegyoon Ahn, Xinshu Xiao

Abstract

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. 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 efficacy in unbiased mapping of the alternative alleles of SNPs and in identification of RNA editing sites. RASER is written in C++ and freely available for download at https://github.com/jaegyoonahn/RASER. gxxiao@ucla.edu Supplementary data are available at Bioinformatics online.

References

Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman
Apr 5, 2002·Genome Research·W James Kent
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Feb 12, 2010·Bioinformatics·Thomas D Wu, Serban Nacu
Jun 23, 2010·Nature Reviews. Genetics·Tomi Pastinen
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Jan 8, 2013·Nature Methods·Gokul RamaswamiJin Billy Li
Aug 24, 2013·BMC Genomics·Ryan M SmithWolfgang Sadee
Oct 15, 2013·Bioinformatics·Franziska ZickmannBernhard Y Renard
Oct 29, 2013·Nucleic Acids Research·Gokul Ramaswami, Jin Billy Li
Nov 5, 2013·Nature Methods·Pär G EngströmUNKNOWN RGASP Consortium
Feb 19, 2015·Nature Biotechnology·Mihaela PerteaSteven L Salzberg
Mar 3, 2015·Nature Methods·Qing Zhang, Xinshu Xiao

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Citations

Oct 4, 2016·Briefings in Bioinformatics·David JohnShizuka Uchida
May 5, 2018·Genome Research·Yun-Hua Esther HsiaoXinshu Xiao
May 30, 2020·Current Protocols in Chemical Biology·Steve D Knutson, Jennifer M Heemstra
Dec 5, 2019·High-throughput·Tyler WeirickShizuka Uchida
Feb 29, 2020·Journal of the American Chemical Society·Steve D KnutsonJennifer M Heemstra

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