Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/84328
Full metadata record
DC FieldValueLanguage
dc.contributor.authorLiu, Yongchao.en
dc.contributor.authorSchmidt, Bertil.en
dc.contributor.authorMaskell, Douglas Leslie.en
dc.date.accessioned2013-06-27T03:04:46Zen
dc.date.accessioned2019-12-06T15:42:49Z-
dc.date.available2013-06-27T03:04:46Zen
dc.date.available2019-12-06T15:42:49Z-
dc.date.copyright2012en
dc.date.issued2012en
dc.identifier.citationLiu, Y., Schmidt, B., & Maskell, D. L. (2012). CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform. Bioinformatics, 28(14), 1830-1837.en
dc.identifier.issn1460-2059en
dc.identifier.urihttps://hdl.handle.net/10356/84328-
dc.description.abstractMotivation: 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. Results: 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.en
dc.language.isoenen
dc.relation.ispartofseriesBioinformaticsen
dc.rights© 2012 The Author.en
dc.subjectDRNTU::Engineering::Computer science and engineeringen
dc.titleCUSHAW : a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transformen
dc.typeJournal Articleen
dc.contributor.schoolSchool of Computer Engineeringen
dc.identifier.doi10.1093/bioinformatics/bts276en
item.fulltextNo Fulltext-
item.grantfulltextnone-
Appears in Collections:SCSE Journal Articles

Google ScholarTM

Check

Altmetric


Plumx

Items in DR-NTU are protected by copyright, with all rights reserved, unless otherwise indicated.