The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.

• FROGS was designed to support multiplexed and demultiplexed sequences.
• FROGS supports 16S, 18S, 23S, ITS and others amplicon reads.
• FROGS supports short or long reads.
• 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 ASV using two methods with a unique multi-affiliation output.
• FROGS offers numerous banks for affiliation step (cf. list ).
• 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.
• To install FROGS: conda or galaxy toolshed.

FROGS was tested on many datasets

• The "FROGS 16S Benchmark tab" and "FROGS ITS Benchmark tab" show comparisons between FROGS and other popular pipelines.