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

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Anton BankevichPavel A Pevzner


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 ( ). It is distributed as open source software.


Jan 1, 1995·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·R M Idury, M S Waterman
Jul 27, 2001·Bioinformatics·P A Pevzner, H Tang
Aug 16, 2001·Proceedings of the National Academy of Sciences of the United States of America·P A PevznerM S Waterman
Sep 3, 2004·Genome Research·Pavel A PevznerGlenn Tesler
Feb 11, 2005·Chemical Reviews·Stephan A Sieber, Mohamed A Marahiel
Jun 3, 2006·Science·Steven R GillKaren E Nelson
Apr 21, 2007·Molecular & Cellular Proteomics : MCP·Nuno BandeiraPavel A Pevzner
Jul 11, 2007·Proceedings of the National Academy of Sciences of the United States of America·Yann MarcyStephen R Quake
Dec 18, 2007·Genome Research·Mark J Chaisson, Pavel A Pevzner
Mar 15, 2008·Genome Research·Jonathan ButlerDavid B Jaffe
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Jun 14, 2008·Current Opinion in Microbiology·Thomas IshoeyRoger S Lasken
Dec 6, 2008·Genome Research·Mark J ChaissonPavel A Pevzner
Dec 9, 2008·Nature Biotechnology·Nuno BandeiraJennie R Lill
Feb 28, 2009·BMC Bioinformatics·Mohammad Sajjad HossainSteven Skiena
Mar 3, 2009·Genome Research·Jared T SimpsonInanç Birol
Jul 11, 2009·Science·Jesse W-H Li, John C Vederas
Sep 3, 2009·PloS One·Sébastien RodrigueSallie W Chisholm
Mar 12, 2010·Genome Biology·David R Kelley, Steven L Salzberg
Apr 30, 2010·PloS One·Tanja WoykeJan-Fang Cheng
Aug 26, 2010·Bioinformatics·Son K Pham, Pavel A Pevzner
Dec 1, 2010·Genome Biology·David R KelleySteven L Salzberg
Dec 1, 2010·Bioinformatics·Lucian IlieSilvana Ilie
Dec 21, 2010·Nature Biotechnology·H Christina FanStephen R Quake
Dec 29, 2010·Proceedings of the National Academy of Sciences of the United States of America·Sante GnerreDavid B Jaffe
Mar 15, 2011·Nature·Nicholas NavinMichael Wigler
Jun 21, 2011·Bioinformatics·Paul MedvedevPavel Pevzner
Sep 13, 2011·Applied and Environmental Microbiology·Noha H YoussefMostafa S Elshahed
Sep 20, 2011·Nature Biotechnology·Hamidreza ChitsazRoger S Lasken
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Methods Mentioned

Single-Cell Sequencing

Software Mentioned

; SC

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