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Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker

Journal article
Authors Johan Bengtsson-Palme
Rodney T Richardson
Marco Meola
Christian Wurzbacher
Émilie D Tremblay
Kärt Kanger
Guillaume J Bilodeau
Reed M Johnson
Martin Hartmann
R. Henrik Nilsson
Published in Bioinformatics (Oxford, England)
Volume 34
Issue 23
Pages 4027–4033
ISSN 1367-4811
Publication year 2018
Published at Department of Biological and Environmental Sciences
Centre for antibiotic resistance research, CARe
Institute of Biomedicine, Department of Infectious Medicine
Pages 4027–4033
Language en
Links dx.doi.org/10.1093/bioinformatics/b...
www.ncbi.nlm.nih.gov/entrez/query.f...
Keywords Metabarcoding ; 16S ; 18S ; ITS ; database builder ; sof
Subject categories Bioinformatics (Computational Biology), Microbiology, Botany, Zoology, Bioinformatics and Systems Biology, Ecology, Biological Systematics, Microbiology in the medical area, Microbiology

Abstract

Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.We evaluated the Metaxa2 Database Builder on eleven commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.Supplementary data are available at Bioinformatics online.

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