784
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

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

      Journal of computational biology : a journal of computational molecular cell biology
      Algorithms, Bacteria, genetics, Genome, Bacterial, Metagenomics, methods, Sequence Analysis, DNA, Single-Cell Analysis

      Read this article at

      ScienceOpenPublisherPMC
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          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.

          Related collections

          Author and article information

          Journal
          22506599
          3342519
          10.1089/cmb.2012.0021

          Chemistry
          Algorithms,Bacteria,genetics,Genome, Bacterial,Metagenomics,methods,Sequence Analysis, DNA,Single-Cell Analysis

          Comments

          Comment on this article