SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
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...
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| Published in | Journal of computational biology Vol. 19; no. 5; p. 455 |
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| Main Authors | , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
01.05.2012
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| Subjects | |
| Online Access | Get more information |
| ISSN | 1557-8666 |
| DOI | 10.1089/cmb.2012.0021 |
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| 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. |
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| AbstractList | 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. |
| Author | Antipov, Dmitry Bankevich, Anton Lesin, Valery M Pham, Son Tesler, Glenn Gurevich, Alexey A Vyahhi, Nikolay Kulikov, Alexander S Pevzner, Pavel A Sirotkin, Alexander V Alekseyev, Max A Dvorkin, Mikhail Pyshkin, Alexey V Nurk, Sergey Prjibelski, Andrey D Nikolenko, Sergey I |
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| SubjectTerms | Algorithms Bacteria - genetics Genome, Bacterial Metagenomics - methods Sequence Analysis, DNA - methods Single-Cell Analysis - methods |
| Title | SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing |
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