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.
Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find, Rapidly, OTUs with Galaxy Solution.
In: ISME-2016 Montreal, CANADA
- 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