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.
authors.affiliation: Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia.
authors.forename: Anton
authors.initials: A
authors.lastname: Bankevich
authors.forename: Sergey
authors.initials: S
authors.lastname: Nurk
authors.forename: Dmitry
authors.initials: D
authors.lastname: Antipov
authors.forename: Alexey A
authors.initials: AA
authors.lastname: Gurevich
authors.forename: Mikhail
authors.initials: M
authors.lastname: Dvorkin
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Kulikov
authors.forename: Valery M
authors.initials: VM
authors.lastname: Lesin
authors.forename: Sergey I
authors.initials: SI
authors.lastname: Nikolenko
authors.forename: Son
authors.initials: S
authors.lastname: Pham
authors.forename: Andrey D
authors.initials: AD
authors.lastname: Prjibelski
authors.forename: Alexey V
authors.initials: AV
authors.lastname: Pyshkin
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Sirotkin
authors.forename: Nikolay
authors.initials: N
authors.lastname: Vyahhi
authors.forename: Glenn
authors.initials: G
authors.lastname: Tesler
authors.forename: Max A
authors.initials: MA
authors.lastname: Alekseyev
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics*; D016680:Genome, Bacterial; D056186:Metagenomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D059010:Single-Cell Analysis / Q000379:methods*