dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes

被引：53

作者：

Safonova, Yana ^{[1
]}

Bankevich, Anton ^{[1
,2
]}

Pevzner, Pavel A. ^{[1
,3
]}

机构：

[1] Russian Acad Sci, Algorithm Biol Lab, St Petersburg Acad Univ, St Petersburg 194021, Russia

[2] St Petersburg State Univ, St Petersburg 199034, Russia

[3] Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA

来源：

JOURNAL OF COMPUTATIONAL BIOLOGY | 2015年 / 22卷 / 06期

基金：

美国国家卫生研究院;

关键词：

de Bruijn graphs; diploid genomes; genome assembly; SPAdes assembler; SEQUENCE; ALGORITHMS; GAUGE;

D O I：

10.1089/cmb.2014.0153

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembly of highly polymorphic (HP) diploid genomes remains challenging. As a result, there is a shortage of tools for assembling HP genomes from the next generation sequencing (NGS) data. The initial approaches to assembling HP genomes were proposed in the pre-NGS era and are not well suited for NGS projects. To address this limitation, we developed the first de Bruijn graph assembler, dipSPAdes, for HP genomes that significantly improves on the state-of-the-art assemblers for HP diploid genomes.

引用

页码：528 / 545

页数：18

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