TY  - JOUR
TI  - SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
AU  - Anton Bankevich
AU  - Sergey Nurk
AU  - Dmitry Antipov
AU  - Alexey Gurevich
AU  - Mikhail Dvorkin
AU  - Alexander S. Kulikov
AU  - Valery M. Lesin
AU  - Sergey Nikolenko
AU  - Son Pham
AU  - Andrey D. Prjibelski
AU  - Alexey Pyshkin
AU  - Alexander Sirotkin
AU  - Nikolay Vyahhi
AU  - Glenn Tesler
AU  - Max A. Alekseyev
AU  - Pavel A. Pevzner
PY  - 2012
JO  - Journal of Computational Biology
DO  - 10.1089/cmb.2012.0021
UR  - https://doi.org/10.1089/cmb.2012.0021
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.
ER  -