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

• Published in: Journal of computational biology Vol. 19; no. 5; p. 455
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: United States 01.05.2012
• Subjects: Algorithms; Bacteria - genetics; Genome, Bacterial; Metagenomics - methods; Sequence Analysis, DNA - methods; Single-Cell Analysis - methods
• ISSN: 1557-8666
• DOI: 10.1089/cmb.2012.0021

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.