METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data.
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 METAXA 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 METAXA - METAXA2 - 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 METAXA2 was compared to other commonly used taxonomic classifiers, showing that METAXA2 often outperforms previous methods in terms of making correct predictions while maintaining a low misclassification rate. METAXA2 is freely available from http://microbiology.se/software/metaxa2/.
Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, 413 46, Gothenburg, Sweden.
Johan
J
Bengtsson-Palme
Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, CH-8903 Birmensdorf, Switzerland.|Molecular Ecology, Institute for Sustainability Sciences, Agroscope, CH-8046 Zurich, Switzerland.
Martin
M
Hartmann
Department of Shipping and Marine Technology, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
Karl Martin
KM
Eriksson
Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, 413 46, Gothenburg, Sweden.
Chandan
C
Pal
Department of Microbiology and Immunology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Box 435, 40530 Gothenburg, Sweden.|Department of Chemical and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden.|Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels Väg 16, 171 77 Stockholm, Sweden.
Kaisa
K
Thorell
Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, 413 46, Gothenburg, Sweden.
Dan Göran Joakim
DG
Larsson
Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden.
Rolf Henrik
RH
Nilsson
D019295:Computational Biology / Q000379:methods*; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D056186:Metagenomics / Q000379:methods*; D012335:RNA, Ribosomal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D004275:DNA, Ribosomal; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012337:RNA, Ribosomal, 18S; D012338:RNA, Ribosomal, 23S; C065096:RNA, ribosomal, 26S
16S; 18S; metagenomics; microbial communities; rRNA libraries; taxonomic assignment