A de novo Genome Assembler based on MapReduce and Bi-directed de Bruijn Graph

被引：0

作者：

Zhang, Yuehua ^{[1
]}

Xuan, Pengfei ^{[1
]}

Wang, Yunsheng ^{[1
]}

Srimani, Pradip K. ^{[1
]}

Luo, Feng ^{[1
]}

机构：

[1] Clemson Univ, Sch Comp, Clemson, SC 29634 USA

来源：

2016 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM) | 2016年

关键词：

next generation sequencing (NGS); assembly; MapReduce; bi-directed de Bruijn graph; ALGORITHMS; PARALLEL;

D O I：

暂无

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

The next generation sequencing (NGS) techniques have enabled biologists to generate large DNA sequences in a high-throughput and low-cost way. Assembly of NGS reads still face great challenges due to the short reads and enormous high volume. In this paper, we presented a new assembler, called GAMR, which is based on bi-directed de Bruijn graph and implemented using MapReduce framework. We designed distributed algorithm for each step in GAMR, making it scalable in assembling large-scale genomes. We evaluated GAMR using GAGE's data and compared it against other NGS assemblers. The results showed GAMR assembled contigs and scaffolds with better accuracy and longer N50 values.

引用

页码：65 / 71

页数：7

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