Metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data
Journal article, 2015

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/

18S

taxonomic assignment

microbial communities

metagenomics

16S

rRNA libraries

Author

Johan Bengtsson-Palme

University of Gothenburg

Martin Hartmann

Eawag - Swiss Federal Institute of Aquatic Science and Technology

Martin Eriksson

Chalmers, Shipping and Marine Technology, Maritime Environmental Sciences

C. Pal

University of Gothenburg

Kaisa Thorell

University of Gothenburg

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

D. G. Joakim Larsson

University of Gothenburg

R. Henrik Nilsson

University of Gothenburg

Molecular Ecology Resources

1755-098X (ISSN) 1755-0998 (eISSN)

Vol. 15 6 1403-1414

Subject Categories

Ecology

Microbiology

Bioinformatics and Systems Biology

DOI

10.1111/1755-0998.12399

PubMed

25732605

More information

Latest update

8/10/2021