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PMID: 22506599 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Journal of computational biology : a journal of computational molecular cell biology ·Vol. 19 ·No. 5 ·2012-05-00 ·Pages 455-77

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA

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.

MeSH Terms

Algorithms Bacteria/genetics Genome, Bacterial Metagenomics/methods Sequence Analysis, DNA/methods Single-Cell Analysis/methods

Authors & Affiliations

16 authors, click to expand affiliations / ORCID

Bankevich Anton

Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia.

Nurk Sergey

Antipov Dmitry

Gurevich Alexey A

Dvorkin Mikhail

Kulikov Alexander S

Lesin Valery M

Nikolenko Sergey I

Pham Son

Prjibelski Andrey D

Pyshkin Alexey V

Sirotkin Alexander V

Vyahhi Nikolay

Tesler Glenn

Alekseyev Max A

Pevzner Pavel A

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Article Info

Journal

Journal of computational biology : a journal of computational molecular cell biology

Abbr.

J Comput Biol

ISSN

1557-8666

DOI

10.1089/cmb.2012.0021

Published

2012-05-00

Epub

2012-00-16

Pages

455-77

Language

English

Region

United States

NLM ID

9433358

PMCID

PMC3342519

Subset

Grants

NCRR NIH HHS · 3P41RR024851-02S1 · United States

External Links

PubMed source DOI: 10.1089/cmb.2012.0021 PMC Full Text View journal details

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SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

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