soapdenovo2 an empirically improved memory-efficient short-read de novo assemblersoapdenovo2一个经验改进节约内存短内容新创汇编.pdf

Luo et al. GigaScience 2012, 1:18 /content/1/1/18 TECHNICAL NOTE Open Access SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler 1,2† 1,2† 1,2,3† 1,2† 1 1 1 Ruibang Luo , Binghang Liu , Yinlong Xie , Zhenyu Li , Weihua Huang , Jianying Yuan , Guangzhu He , 1 1 1 1 1 1 1 1 Yanxiang Chen , Qi Pan , Yunjie Liu , Jingbo Tang , Gengxiong Wu , Hao Zhang , Yujian Shi , Yong Liu , 1 1 1 1 2 2 4 4 Chang Yu , Bo Wang , Yao Lu , Changlei Han , David W Cheung , Siu-Ming Yiu , Shaoliang Peng , Zhu Xiaoqian , 4 4 1,2 1 1 2* 1* Guangming Liu , Xiangke Liao , Yingrui Li , Huanming Yang , Jian Wang , Tak-Wah Lam and Jun Wang Abstract Background: There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. Findings: To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and