The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. It produces abundance table of OTUs and their taxonomic affiliation.
- FROGS was designed to support multiplexed and demultiplexed sequences.
- The preprocessing tool is dedicated to paired sequences merging, cleaning and dereplication.
- The clustering tool uses Swarm with a local clustering threshold, not a global clustering threshold like other software do.
- Chimera removal tool uses VSEARCH combined with an innovative chimera cross-validation.
- A filtering tool allows to remove noisy data.
- Affiliation tool returns taxonomic affiliation for each OTU using two methods with a unique multi-affiliation output.
- A lot of statistical results and numerous graphical illustrations are also produced.
- FROGS is designed for non-specialists thanks to its Galaxy interface, but is also available with command lines github.
- Its tools can be used independently, or as a workflow.
- It is portable on all Galaxy platforms with few informatics requirements and architecture dependencies.
FROGS was tested on many datasets
- the followed tabs show comparisons between FROGS, MOTHUR, UPARSE and QIIME, the popular pipelines.
Frédéric Escudié, Lucas Auer, Maria Bernard, Mahendra Mariadassou, Laurent Cauquil, Katia Vidal, Sarah Maman, Guillermina Hernandez-Raquet, Sylvie Combes, Géraldine Pascal; FROGS: Find, Rapidly, OTUs with Galaxy Solution, Bioinformatics, Volume 34, Issue 8, 15 April 2018, Pages 1287–1294
- Request an account to genotoul bionfo platform via a form Genotoul Platform
- Enter your credential (once for apache server connexion and a second times for galaxy platform connexion): Galaxy Server (on the top) /user /login
- Get data: In silico simulated data (4th history of the documentation below - from exercise 3.3)
- Play with this workflow: Workflow Test and import it on your account (green cross on the top).
- To learn more: Formation documentation