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.
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U2 - 10.1089/cmb.2012.0021
DO - 10.1089/cmb.2012.0021
M3 - Article
C2 - 22506599
AN - SCOPUS:84860771820
SN - 1066-5277
VL - 19
SP - 455
EP - 477
JO - Journal of Computational Biology
JF - Journal of Computational Biology
IS - 5
ER -