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 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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References in zbMATH (referenced in 2 articles )
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- Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
- Komusiewicz, Christian; Radulescu, Andreea: On the sound covering cycle problem in paired de Bruijn graphs (2015)