生物信息学2011，Vol.9Issue(2)：106-112,7.DOI:10.3969/j.issn.1672-5565.2011.02.004
四种常用高通量测序拼接软件的应用比较
Comparison of the widely used high-throughput sequencing assembly software
摘要
Abstract
The emergence of new sequencing platforms led to resurgence of research in whole - genome shotgun assembly algorithms and software. Since 2005 , several assembly software packages had been develpoed for de novo assembly of high - throughput sequencing data, and have been constantly made improvements to enhance the output of assembly. In this paper, the widely used high - thruughput sequencing assembly software packages, namely Velvet, AbySS, SOAPdenovo and CLC were used to assembly high - throughput sequencing data of a novo T4 - like bacteriophage IMF08 derived by Solexa Genome Analyzer. For every individual package, various parameters and input raw data size were evaluated to find out the optimized assembly conditions , and the assembly results of different software packages were compared. . Our data showed that all the four software package are able to assemble the 172kb full length genome , but with different raw sequencing sizes and different parameters. Our experiences could serve as a reference for other researchers to use these software packages.关键词
第二代测序/从头拼接/Velvet/ABySS/SOAPdenovo/CLC Genomic WorkbenchKey words
Next - Gen sequencing/ de novo assembly/ Velvet/ AbySS/ SOAPdenovo/ CLC Genomic Workbench分类
生物科学引用本文复制引用
朱大强,李存,陈斌,姜焕焕,江晓芳,安小平,米志强,陈禹保,童贻刚..四种常用高通量测序拼接软件的应用比较[J].生物信息学,2011,9(2):106-112,7.基金项目
国家高技术研究发展计划项目(2009AA02Z111) （2009AA02Z111）
国家科技重大专项基金(2008ZX10001-013). （2008ZX10001-013）
