Tax4Fun

MOTIVATION: The characterization of phylogenetic and functional diversity is a
key element in the analysis of microbial communities. Amplicon-based sequencing
of marker genes, such as 16S rRNA, is a powerful tool for assessing and comparing
the structure of microbial communities at a high phylogenetic resolution. Because
16S rRNA sequencing is more cost-effective than whole metagenome shotgun
sequencing, marker gene analysis is frequently used for broad studies that
involve a large number of different samples. However, in comparison to shotgun
sequencing approaches, insights into the functional capabilities of the community
get lost when restricting the analysis to taxonomic assignment of 16S rRNA data.
RESULTS: Tax4Fun is a software package that predicts the functional capabilities
of microbial communities based on 16S rRNA datasets. We evaluated Tax4Fun on a
range of paired metagenome/16S rRNA datasets to assess its performance. Our
results indicate that Tax4Fun provides a good approximation to functional
profiles obtained from metagenomic shotgun sequencing approaches. AVAILABILITY
AND IMPLEMENTATION: Tax4Fun is an open-source R package and applicable to output
as obtained from the SILVAngs web server or the application of QIIME with a SILVA
database extension. Tax4Fun is freely available for download at
http://tax4fun.gobics.de/. CONTACT: kasshau@gwdg.de SUPPLEMENTARY INFORMATION:
Supplementary data are available at Bioinformatics online.

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data.

Tax4Fun is a software package that predicts the functional capabilities of microbial communities based on 16S rRNA datasets. The tool is an open-source R package that provides a good approximation to functional profiles obtained from metagenomic shotgun sequencing approaches. It is applicable to output as obtained from the SILVAngs web server or the application of QIIME with a SILVA database extension.

Tax4Fun

Topic

Detail

Publications

Download and documentation