Journal
JOURNAL OF COMPUTATIONAL BIOLOGY
Volume 19, Issue 5, Pages 455-477Publisher
MARY ANN LIEBERT, INC
DOI: 10.1089/cmb.2012.0021
Keywords
assembly; de Bruijn graph; single cell; sequencing; bacteria
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Funding
- Government of the Russian Federation [11.G34.31.0018]
- National Institutes of Health [3P41RR024851-02S1]
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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 un-cultivatable 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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