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Journal Articles Bioinformatics Year : 2012

SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.

Abstract

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 tasks to distinguish among these and to further categorize the families of messenger RNAs and ribosomal RNAs is an important step for examining gene expression patterns of an interactive environment and the phylogenetic classification of the constituting species. RESULTS: We present SortMeRNA, a new software designed to rapidly filter ribosomal RNA 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. AVAILABILITY: http://bioinfo.lifl.fr/RNA/sortmerna CONTACT: evguenia.kopylova@lifl.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Dates and versions

hal-00748990 , version 1 (16-12-2013)

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Evguenia Kopylova, Laurent Noé, Héléne Touzet. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.. Bioinformatics, 2012, 28 (24), pp.3211-3217. ⟨10.1093/bioinformatics/bts611⟩. ⟨hal-00748990⟩
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