Genome Assembly - SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

 At 2013-09-26 12:31:09 AM  |   419

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 (https://bioinf.spbau.ru/spades). It is distributed as open source software.

Read more athttps://online.liebertpub.com/doi/abs/10.1089/cmb.2012.0021 

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