SOAP：短寡核苷酸比对程序。

SOAP: short oligonucleotide alignment program.

作者信息

Li Ruiqiang, Li Yingrui, Kristiansen Karsten, Wang Jun

机构信息

Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China.

出版信息

Bioinformatics. 2008 Mar 1;24(5):713-4. doi: 10.1093/bioinformatics/btn025. Epub 2008 Jan 28.

DOI:10.1093/bioinformatics/btn025

PMID:18227114

Abstract

SUMMARY

We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets.

AVAILABILITY

http://soap.genomics.org.cn.

摘要

我们开发了一个名为SOAP的程序，用于将短寡核苷酸高效地比对到参考序列上，包括有间隙和无间隙比对。该程序旨在处理使用新一代Illumina-Solexa测序技术通过平行测序产生的大量短读段。SOAP与众多应用兼容，包括单端或双端重测序、小RNA发现以及mRNA标签序列定位。SOAP是一个命令驱动的程序，支持多线程并行计算，并且有一个用于多个查询集的批处理模块。