SPAdes: a New Genome Assembly Algorithm and Its Applications to Single-cell Sequencing

Overview

Journal J Comput Biol

Specialties Biology
Molecular Biology

Date 2012 Apr 18

PMID 22506599

Citations 12786

Authors

Anton Bankevich

Sergey Nurk

Dmitry Antipov

Alexey A Gurevich

Mikhail Dvorkin

Alexander S Kulikov

Valery M Lesin

Sergey I Nikolenko

Son Pham

Andrey D Prjibelski

Alexey V Pyshkin

Alexander V Sirotkin

Nikolay Vyahhi

Glenn Tesler

Max A Alekseyev

Pavel A Pevzner

Affiliations

Soon will be listed here.

Abstract

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 uncultivatable 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.

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