http://dx.doi.org/10.1093/bioinformatics/bts061">
 

Document Type

Journal Article

Department/Unit

Department of Computer Science

Title

SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads

Language

English

Abstract

SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes < 30 s to align a million read pairs onto the human reference genome and is at least 7.5 and 20 times faster than BWA and Bowtie, respectively. For aligning reads with up to four mismatches, SOAP3 aligns slightly more reads than BWA and Bowtie; this is because SOAP3, unlike BWA and Bowtie, is not heuristic-based and always reports all answers. © The Author 2012. Published by Oxford University Press. All rights reserved.

Publication Date

2012

Source Publication Title

Bioinformatics

Volume

28

Issue

6

Start Page

878

End Page

879

Publisher

Oxford University Press

ISSN (print)

13674803

ISSN (electronic)

14602059

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