Biologists interested in microbiota from various environments (gut, soil, aquatic, food, etc.) use genetic markers to understand their composition and follow their evolution – the metabarcoding. FROGS [1] is a software package for accurate, simple and robust processing of metabarcoding sequencing reads. FROGS uses standard methods and tools combined with original and innovative approaches (such as the support of yeast and fungal markers [2]). In addition to the expected outputs (abundance table of the species in the environment and their affiliations), FROGS offers numerous graphs and statistics allowing biologists to enrich their analyses. Its use is open to both non-experts and experts thanks to the launch of the tools via the Galaxy platforms or via the command line.
FROGS is dedicated to researchers in biology (medicine, environment, agriculture, health, food) in its analysis objectives and in its use. It has currently been downloaded more than 8650 times and has been cited many times in scientific publications. https://scholar.google.com/scholar?oi=bibs&hl=fr&cites=9337335053143310824&as_sdt=5
Prestigious journals with very high impact factor cite FROGS i.e. Nature, Nature Medicine, Current Biology, Cell report etc. FROGS is therefore a very important tool and fully participates in the scientific advances in microbial ecology.
A virtuous circle is created between research and software development. Indeed, the constant progress of sequencing techniques allows researchers to ask new questions that they can answer. We adapt and enrich FROGS with new capabilities and tools. For the past 7 years, we have been constantly expanding the community served by offering new potential to FROGS.
Examples of improvements based on researches: the treatment of fungal and yeast markers in addition to the classic bacterial markers (adaptation of 2 tools and addition of one); or the development of statistical tools allowing data to be processed by R via a graphical interface without going through the command line (addition of 9 tools); or the creation of 4 applications allowing the functional potential of the microbial community studied to be revealed (based on Picrust2).
Where to find FROGS ?
Github: https://github.com/geraldinepascal/FROGS.git and https://github.com/geraldinepascal/FROGS-wrappers
BioConda: https://anaconda.org/bioconda/frogs
toolshed Galaxy: https://toolshed.g2.bx.psu.edu/view/frogs/frogs/834843ebe569
All Galaxy platforms that have installed FROGS scattered around the world e.g. http://vm-galaxy-prod.toulouse.inra.fr/ and https://galaxy.migale.inra.fr/
[1] : https://doi.org/10.1093/bioinformatics/btx791 Escudié et al. “Find, Rapidly, OTUs with Galaxy Solution”, Bioinformatics, Volume 34, Issue 8, 15 April 2018, Pages 1287–1294
[2] : https://doi.org/10.1093/bib/bbab318 Bernard et al. “FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers”, Briefings in Bioinformatics 2021, 10.1093/bib/bbab318