A de novo assembly method for metagenomic DNA reads with mate pairs
A high quality assembly of reads, which are short fragments generated from shotgun sequencing, is a substantial part of the metagenome projects. Although traditional assemblers have been employed in initial analysis of the metagenomes, they cannot surmount the challenges created by the features of metagenomic data. We present a de novo assembly algorithm for metagenomes with mate pairs. Our method uses mate pair information to guide contig construction. More specifically, we developed an efficient algorithm to find the best mate pair threading paths from the overlap graph to construct contigs. Tests on simulated metagenome data show that our method produced more accurate assembly than Celera Assembler and Phrap when assembling contigs at a same level.
component metagenome sequence assembly de novo algorithm overlap graph mate pairs
Binbin Lai Ruogu Ding Huaiqiu Zhu
State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University Center for Theoretical Biology of AAIS, Peking University Beijing 100871, China
国际会议
上海
英文
1574-1578
2011-10-15（万方平台首次上网日期，不代表论文的发表时间）