SOAP2: an improved ultrafast tool for short read alignment

被引：2852

作者：

Li, Ruiqiang ^{[1
,2
]}

Yu, Chang ^{[1
]}

Li, Yingrui ^{[1
]}

Lam, Tak-Wah ^{[3
]}

Yiu, Siu-Ming ^{[3
]}

Kristiansen, Karsten ^{[2
]}

Wang, Jun ^{[1
,2
]}

机构：

[1] Beijing Genom Inst Shenzhen, Shenzhen 518083, Peoples R China

[2] Univ So Denmark, Dept Biochem & Mol Biol, DK-5230 Odense M, Denmark

[3] Univ Hong Kong, Dept Comp Sci, Hong Kong, Hong Kong, Peoples R China

来源：

BIOINFORMATICS | 2009年 / 25卷 / 15期

基金：

中国国家自然科学基金;

关键词：

GENOME; DNA;

D O I：

10.1093/bioinformatics/btp336

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 5.4GB 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. le formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome.

引用

页码：1966 / 1967

页数：2

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