计算机科学
搜索引擎索引
转化(遗传学)
参考基因组
多序列比对
基因组学
序列比对
基因组
情报检索
生物
遗传学
基因
作者
Ruiqiang Li,Chang Sik Yu,Yingrui Li,Tak-Wah Lam,Siu-Ming Yiu,Karsten Kristiansen,Jun Wang
出处
期刊:Bioinformatics
[Oxford University Press]
日期:2009-08-01
卷期号:25 (15): 1966-1967
被引量:3140
标识
DOI:10.1093/bioinformatics/btp336
摘要
Abstract Summary: 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. Availability: http://soap.genomics.org.cn Contact: soap@genomics.org.cn
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