SOAP2: an improved ultrafast tool for short read alignment

Li, Ruiqiang, Yu, Chang, Li, Yingrui, Lam, Tak-Wah, Yiu, Siu-Ming, Kristiansen, Karsten and Wang, Jun (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25 15: 1966-1967. doi:10.1093/bioinformatics/btp336

Author Li, Ruiqiang
Yu, Chang
Li, Yingrui
Lam, Tak-Wah
Yiu, Siu-Ming
Kristiansen, Karsten
Wang, Jun
Title SOAP2: an improved ultrafast tool for short read alignment
Journal name Bioinformatics   Check publisher's open access policy
ISSN 1367-4803
Publication date 2009-08-01
Year available 2009
Sub-type Article (original research)
DOI 10.1093/bioinformatics/btp336
Open Access Status Not Open Access
Volume 25
Issue 15
Start page 1966
End page 1967
Total pages 2
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Abstract SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
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