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1070520 
Journal Article 
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing 
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 
2012 
Yes 
Journal of Computational Biology
ISSN: 1066-5277
EISSN: 1557-8666 
19 
5 
455-477 
English 
22506599 
WOS:000303811800001 
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.