Frédéric Escudié1, Lucas Auer2, Maria Bernard3, Mahendra Mariadassou4, Laurent Cauquil5, Katia Vidal5, Sarah Maman5, Guillermina Hernandez-Raquet6, Sylvie Combes5, Géraldine Pascal5. 1. Bioinformatics platform Toulouse Midi-Pyrenees, MIAT, INRA Auzeville CS 52627 31326 Castanet Tolosan cedex, France. 2. INRA, UMR 1136, Université de Lorraine, INRA-Nancy, 54280, Champenoux, France. 3. GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France. 4. MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France. 5. GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France. 6. Laboratoire d'ingénierie des Systèmes Biologiques et des Procédés-LISBP, Université de Toulouse, INSA, INRA, CNRS, Toulouse, France.
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.
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.
Authors: Neal B Shah; Andrew S Allegretti; Sagar U Nigwekar; Sahir Kalim; Sophia Zhao; Benjamin Lelouvier; Florence Servant; Gloria Serena; Ravi Ishwar Thadhani; Dominic S Raj; Alessio Fasano Journal: Clin J Am Soc Nephrol Date: 2019-04-08 Impact factor: 8.237
Authors: M Minty; P Loubières; T Canceill; V Azalbert; R Burcelin; F Tercé; V Blasco-Baque Journal: J Physiol Biochem Date: 2020-07-09 Impact factor: 4.158