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SPAdes : A new genome assembly algorithm and its applications to single-cell sequencing. / Bankevich, Anton; 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.

в: Journal of Computational Biology, Том 19, № 5, 01.05.2012, стр. 455-477.

Результаты исследований: Научные публикации в периодических изданиях › статья › Рецензирование

Author

Bankevich, Anton ; 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. / SPAdes : A new genome assembly algorithm and its applications to single-cell sequencing. в: Journal of Computational Biology. 2012 ; Том 19, № 5. стр. 455-477.

BibTeX

@article{5524318ff6b84b3ea20635d3d6374718,

title = "SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing",

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.",

keywords = "assembly, bacteria, de Bruijn graph, sequencing, single cell",

author = "Anton Bankevich and Sergey Nurk and Dmitry Antipov and Gurevich, {Alexey A.} and Mikhail Dvorkin and Kulikov, {Alexander S.} and Lesin, {Valery M.} and Nikolenko, {Sergey I.} and Son Pham and Prjibelski, {Andrey D.} and Pyshkin, {Alexey V.} and Sirotkin, {Alexander V.} and Nikolay Vyahhi and Glenn Tesler and Alekseyev, {Max A.} and Pevzner, {Pavel A.}",

year = "2012",

month = may,

day = "1",

doi = "10.1089/cmb.2012.0021",

language = "English",

volume = "19",

pages = "455--477",

journal = "Journal of Computational Biology",

issn = "1066-5277",

publisher = "Mary Ann Liebert Inc.",

number = "5",

}

RIS

TY - JOUR

T1 - SPAdes

T2 - A new genome assembly algorithm and its applications to single-cell sequencing

AU - Bankevich, Anton

AU - Nurk, Sergey

AU - Antipov, Dmitry

AU - Gurevich, Alexey A.

AU - Dvorkin, Mikhail

AU - Kulikov, Alexander S.

AU - Lesin, Valery M.

AU - Nikolenko, Sergey I.

AU - Pham, Son

AU - Prjibelski, Andrey D.

AU - Pyshkin, Alexey V.

AU - Sirotkin, Alexander V.

AU - Vyahhi, Nikolay

AU - Tesler, Glenn

AU - Alekseyev, Max A.

AU - Pevzner, Pavel A.

PY - 2012/5/1

Y1 - 2012/5/1

N2 - 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.

AB - 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.

KW - assembly

KW - bacteria

KW - de Bruijn graph

KW - sequencing

KW - single cell

UR - http://www.scopus.com/inward/record.url?scp=84860771820&partnerID=8YFLogxK

U2 - 10.1089/cmb.2012.0021

DO - 10.1089/cmb.2012.0021

M3 - Article

C2 - 22506599

VL - 19

SP - 455

EP - 477

JO - Journal of Computational Biology

JF - Journal of Computational Biology

SN - 1066-5277

IS - 5

ER -

ID: 5518803

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

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