Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data

By K. Aßhauer, Bernd Wemheuer, Rolf Daniel, Peter Meinicke. Bioinform., 2015

1,368 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2f34616ea61be60413125f183bcf878bae3d7757

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Citations in the corpus

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences (2020, methodology): “In past years, several freely available tools including PICRUSt [22], Tax4Fun [23], Piphillin [24], Faprotax [25] and paprica [26] have been developed for the prediction of functional profiles inferred from 16S rRNA gene sequence data.”
MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data (2017, methodology): “In particular, the PICRUSt is used for Greengenes annotated data (23) and the Tax4Fun is used for data annotated by SILVA database (24).”
Current challenges and best-practice protocols for microbiome analysis (2019, methodology): “While Tax4Fun is an R-based algorithm utilizing SILVA as reference, PICRUSt is a bioinformatics pipeline that clusters protein sequences based on KEGG or COG gene families and 16S rRNA gene copy numbers.”