Metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. (23rd March 2015)

• Record Type: Journal Article
• Authors: Bengtsson‐Palme, Johan; Hartmann, Martin; Eriksson, Karl Martin; Pal, Chandan; Thorell, Kaisa; Larsson, Dan Göran Joakim; Nilsson, Rolf Henrik
• Is Part Of: Molecular ecology resources. Volume 15:Number 6(2015:Nov.)
• Page Start: 1403
• Page End: 1414
• Publication Date: 2015-03-23
• Subjects: Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.12399
• Languages: English
• ISSNs: 1755-098X

Abstract

<abstract abstract-type="main" id="men12399-abs-0001"> <title>Abstract</title> <p>The ribosomal rRNA genes are widely used as genetic markers for taxonomic identification of microbes. Particularly the small subunit (SSU; 16S/18S) rRNA gene is frequently used for species‐ or genus‐level identification, but also the large subunit (LSU; 23S/28S) rRNA gene is employed in taxonomic assignment. The <sc>metaxa</sc> software tool is a popular utility for extracting partial rRNA sequences from large sequencing data sets and assigning them to an archaeal, bacterial, nuclear eukaryote, mitochondrial or chloroplast origin. This study describes a comprehensive update to <sc>metaxa</sc> – <sc>metaxa</sc>2 – that extends the capabilities of the tool, introducing support for the LSU rRNA gene, a greatly improved classifier allowing classification down to genus or species level, as well as enhanced support for short‐read (100 bp) and paired‐end sequences, among other changes. The performance of <sc>metaxa</sc>2 was compared to other commonly used taxonomic classifiers, showing that <sc>metaxa</sc>2 often outperforms previous methods in terms of making correct predictions while maintaining a low misclassification rate. <sc>metaxa</sc>2 is freely available from <ext-link ext-link-type="uri" xlink:href="http://microbiology.se/software/metaxa2/" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">http://microbiology.se/software/metaxa2/</ext-link>.</p> </abstract>