828
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: not found
      • Article: not found

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

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          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
          Journal of Computational Biology
          Journal of Computational Biology
          Mary Ann Liebert Inc
          1066-5277
          1557-8666
          May 2012
          May 2012
          : 19
          : 5
          : 455-477
          Affiliations
          [1 ]Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia.
          [2 ]These authors contributed equally to this work.
          [3 ]Steklov Institute of Mathematics, St. Petersburg, Russia.
          [4 ]Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California.
          [5 ]Department of Mathematics, University of California, San Diego, La Jolla, California.
          [6 ]Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina.
          Article
          10.1089/cmb.2012.0021
          3342519
          22506599
          edfc2c93-ecbc-4462-8791-dc0d70640c47
          © 2012

          http://www.liebertpub.com/nv/resources-tools/text-and-data-mining-policy/121/

          History

          Comments

          Comment on this article