CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform

Bioinformatics
Yongchao LiuDouglas L Maskell

Abstract

New high-throughput sequencing technologies have promoted the production of short reads with dramatically low unit cost. The explosive growth of short read datasets poses a challenge to the mapping of short reads to reference genomes, such as the human genome, in terms of alignment quality and execution speed. We present CUSHAW, a parallelized short read aligner based on the compute unified device architecture (CUDA) parallel programming model. We exploit CUDA-compatible graphics hardware as accelerators to achieve fast speed. Our algorithm uses a quality-aware bounded search approach based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini index to reduce the search space and achieve high alignment quality. Performance evaluation, using simulated as well as real short read datasets, reveals that our algorithm running on one or two graphics processing units achieves significant speedups in terms of execution time, while yielding comparable or even better alignment quality for paired-end alignments compared with three popular BWT-based aligners: Bowtie, BWA and SOAP2. CUSHAW also delivers competitive performance in terms of single-nucleotide polymorphism calling for an Escherichia coli test dataset. http://cushaw.s...Continue Reading

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Citations

Sep 11, 2012·Bioinformatics·Yongchao Liu, Bertil Schmidt
Feb 28, 2013·BMC Bioinformatics·Yupeng ChenDouglas L Maskell
Jun 7, 2013·PloS One·Ruibang LuoTak-Wah Lam
May 21, 2014·PloS One·Andrea ManconiLuciano Milanesi
Apr 11, 2014·BMC Bioinformatics·Peter KerpedjievAnders Krogh
Jan 28, 2014·Bioinformatics·Kaiyong Zhao, Xiaowen Chu
Aug 26, 2014·BioMed Research International·Claudia MisaleMarco Aldinucci
Jul 6, 2014·Bioinformatics·Erwan DrezenDominique Lavenier
Feb 24, 2016·Frontiers in Genetics·Daniel LangenkämperTim W Nattkemper
Oct 10, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Alejandro ChacónJuan Carlos Moure
Nov 30, 2012·IEEE Reviews in Biomedical Engineering·May Dongmei Wang
Mar 26, 2015·Frontiers in Bioengineering and Biotechnology·Andrea ManconiLuciano Milanesi
Jun 15, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yongchao LiuBertil Schmidt
Jul 13, 2016·Briefings in Bioinformatics·Marco S NobileDaniela Besozzi
Sep 27, 2016·International Journal of Molecular Sciences·Han MiaoXingfang Gu
Nov 4, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·David NogueiraNuno Roma
Jan 6, 2016·PloS One·Jorge González-DomínguezBertil Schmidt
Apr 6, 2017·Bioinformatics·Hsin-Nan Lin, Wen-Lian Hsu
Mar 10, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·James ArramPeiyong Jiang
Jan 1, 2014·Cancer Informatics·Pankaj Agarwal, Kouros Owzar
Jul 1, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ahmad Al KawamAniruddha Datta
Feb 26, 2014·BMC Bioinformatics·Andrea ManconiLuciano Milanesi
May 28, 2015·Genome Medicine·Song Ling PoonSteven G Rozen
Jan 10, 2018·Scientific Reports·Pål TrosvikAddisu Mekonnen
Mar 14, 2020·BMC Bioinformatics·Robin KobusBertil Schmidt
May 12, 2019·Scientific Reports·Konstantinos Prousalis, Nikos Konofaos

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