SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

被引：18721

作者：

Bankevich, Anton ^{[2
]}

Nurk, Sergey ^{[2
]}

Antipov, Dmitry ^{[2
]}

Gurevich, Alexey A. ^{[2
]}

Dvorkin, Mikhail ^{[2
]}

Kulikov, Alexander S. ^{[2
,3
]}

Lesin, Valery M. ^{[2
]}

Nikolenko, Sergey I. ^{[2
,3
]}

Son Pham ^{[4
]}

Prjibelski, Andrey D. ^{[2
]}

Pyshkin, Alexey V. ^{[2
]}

Sirotkin, Alexander V. ^{[2
]}

Vyahhi, Nikolay ^{[2
]}

Tesler, Glenn ^{[5
]}

Alekseyev, Max A. ^{[1
,2
]}

Pevzner, Pavel A. ^{[2
,4
]}

机构：

[1] Univ S Carolina, Dept Comp Sci & Engn, Columbia, SC 29208 USA

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

[3] VA Steklov Math Inst, St Petersburg 191011, Russia

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

[5] Univ Calif San Diego, Dept Math, La Jolla, CA 92093 USA

来源：

JOURNAL OF COMPUTATIONAL BIOLOGY | 2012年 / 19卷 / 05期

基金：

美国国家卫生研究院;

关键词：

assembly; de Bruijn graph; single cell; sequencing; bacteria; DE-BRUIJN GRAPHS; BACTERIAL GENOMES; AMPLIFICATION; MATTER;

D O I：

10.1089/cmb.2012.0021

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of un-cultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software.

引用

页码：455 / 477

页数：23

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