SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

DOI PDF 28 Citations
  • Evguenia Kopylova
    1 LIFL (UMR CNRS 8022 Université Lille 1) and 2Inria Lille Nord-Europe, 59655 Villeneuve d'Ascq, France
  • Laurent Noé
    1 LIFL (UMR CNRS 8022 Université Lille 1) and 2Inria Lille Nord-Europe, 59655 Villeneuve d'Ascq, France
  • Hélène Touzet
    1 LIFL (UMR CNRS 8022 Université Lille 1) and 2Inria Lille Nord-Europe, 59655 Villeneuve d'Ascq, France

Description

<jats:title>Abstract</jats:title> <jats:p>Motivation: The application of next-generation sequencing (NGS) technologies to RNAs directly extracted from a community of organisms yields a mixture of fragments characterizing both coding and non-coding types of RNAs. The task to distinguish among these and to further categorize the families of messenger RNAs and ribosomal RNAs (rRNAs) is an important step for examining gene expression patterns of an interactive environment and the phylogenetic classification of the constituting species.</jats:p> <jats:p>Results: We present SortMeRNA, a new software designed to rapidly filter rRNA fragments from metatranscriptomic data. It is capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time.</jats:p> <jats:p>Availability:  http://bioinfo.lifl.fr/RNA/sortmerna</jats:p> <jats:p>Contact:  evguenia.kopylova@lifl.fr</jats:p> <jats:p>Supplementary information:  Supplementary data are available at Bioinformatics online.</jats:p>

Journal

  • Bioinformatics

    Bioinformatics 28 (24), 3211-3217, 2012-10-15

    Oxford University Press (OUP)

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