SOAP2: an improved ultrafast tool for short read alignment
SOAP2: an improved ultrafast tool for short read alignment
复制标题
SOAP2：改进的超快工具，用于短读对齐
DOI：
10.1093/bioinformatics/btp336
复制
发表时间：
2009-08-01
期刊：
影响因子：
5.8
通讯作者：
Wang, Jun
中科院分区：
文献类型：
--
作者：
Li, Ruiqiang;Yu, Chang;Wang, Jun
总结
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.