Dataset Information
MetAmp: combining amplicon data from multiple markers for OTU analysis.
Ontology highlight
ABSTRACT: Motivation
We present a novel method and corresponding application, MetAmp, to combine amplicon data from multiple genomic markers into Operational Taxonomic Units (OTUs) for microbial community analysis, calibrating the markers using data from known microbial genomes. When amplicons for multiple markers such as the 16S rRNA gene hypervariable regions are available, MetAmp improves the accuracy of OTU-based methods for characterizing bacterial composition and community structure. MetAmp works best with at least three markers, and is applicable to non-bacterial analyses and to non 16S markers. Our application and testing have been limited to 16S analysis of microbial communities.Results
We clustered standard test sequences derived from the Human Microbiome Mock Community test sets and compared MetAmp and other tools with respect to their ability to recover OTUs for these benchmark bacterial communities. MetAmp compared favorably to QIIME, UPARSE and Mothur using amplicons from one, two, and three markers.Availability and implementation
MetAmp is available at http://izhbannikov.github.io/MetAmp/.
SUBMITTER: Zhbannikov IY
PROVIDER: S-EPMC4443678 | biostudies-literature | 2015 Jun
REPOSITORIES: biostudies-literature
Publications
MetAmp: combining amplicon data from multiple markers for OTU analysis.
Bioinformatics (Oxford, England) 20150127 11
<h4>Motivation</h4>We present a novel method and corresponding application, MetAmp, to combine amplicon data from multiple genomic markers into Operational Taxonomic Units (OTUs) for microbial community analysis, calibrating the markers using data from known microbial genomes. When amplicons for multiple markers such as the 16S rRNA gene hypervariable regions are available, MetAmp improves the accuracy of OTU-based methods for characterizing bacterial composition and community structure. MetAmp ...[more]