FROGS : Find, Rapidly, OTUs with Galaxy Solution

TitleFROGS : Find, Rapidly, OTUs with Galaxy Solution
Publication TypeJournal Article
Year of Publication2018
AuthorsEscudié, F, Auer, L, Bernard, M, Mariadassou, M, Cauquil, L, Vidal, K, Maman, S, Hernandez-Raquet, G, Combes, S, Pascal, G
JournalBioinformatics
Volume34
Issue8
Pagination1287-1294
Date Published2018 Apr 15
ISSN1367-4811
Abstract

Motivation: Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own.Results: This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME.Availability and implementation: Source code and instructions for installation: https://github.com/geraldinepascal/FROGS.git. A companion website: http://frogs.toulouse.inra.fr.Contact: geraldine.pascal@inra.fr.Supplementary information: Supplementary data are available at Bioinformatics online.

DOI10.1093/bioinformatics/btx791
Alternate JournalBioinformatics
PubMed ID29228191