October 2022 - FROGS News
- FROGS v4.0.1 is available
- What has changed since the last version?
- Tools added, Modified tools: Normalisation tool; OTU_filter tool; Affiliation_stat tool; Remove_chimera tool
- New documentations for using FROGS v4.0.1
- New databases are available
- You need help to use FROGS, you are looking for training
- Who uses FROGS?
June 2021 - FROGS News
April 2019 - FROGS News
December 2018 - FROGS NewsThe FROGS team wishes you a very happy holiday season. And for Christmas, we offer you our FROGS playlist
You can also find it on our website on FAQ on the FROGS website.
Have a good listening !
November 2018 - FROGS NewsFROGS 3.0 has just been published on github : https://github.com/geraldinepascal/FROGS/releases
The new version of FROGS, now, supports ITS sequences.
This new version consists of:
- The modification of the "Preprocess Tool"
- to take into account ITS reads which could have the particularity of having non-overlapping reads
- to take into account the overlapping reads of all types
- we added the VSEARCH software for merging reads
- loss of the " Expected amplicon size" parameter with the VSEARCH tool
- possibility to use PEAR in command line only for merging overlapping reads but only and only if you have the license or if you belong to the academic world.
- A new graphic charter for HTML outputs
- A new "ITSx" tool that identifies and extracts ITS regions
- To affiliate ITS, a new sequence affiliation strategy has been implemented. Adding needleall software
- A new affiliation processing tool "Affiliation post-process Tool» allows OTUs to be merged together according to criteria of percentage of identity and coverage with referential affiliation.
Please be particularly attentive to the “FROGS_combined” section.
April 2018 - FROGS NewsThe FROGS article having just been published on 15 April 2018 in paper version, the reference to the article has evolved.
You must now quote the article as follows:
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, https://doi.org/10.1093/bioinformatics/btx791
You will find here a link to the article : Article (free access)
January 2018 - FROGS NewsIn the new Silva version 132, many phyla in bacteria are rearranged following the Genome Taxonomy Database.
Proteobacteria drastically rearranged. Epsilonproteobacteria are own phylum, Betaproteobacteria now an order of Gammaproteobacteria.
For more details, see Silva release notes: https://www.arb-silva.de/documentation/release-132/
December 2017 - FROGS NewsThe Silva 132 is now available in FROGS.
You can choose between silva 16S, 18S and 23S.
As well as Silva 16S filtered with pintail equal to 50, 80 or 100.
The unfiltered 16S silva on the pintail appears by default in the "Affiliation" tool of Galaxy Sigenae of Toulouse.
For Galaxy admin, the banks are available at http://genoweb.toulouse.inra.fr/frogs_databanks/assignation
And the implementation procedure is described in the Github Readme https://github.com/geraldinepascal/FROGS#8-upload-and-configure-the-databanks
We remind you that the SILVA is not free of rights for non-academic people. Please refer to the license terms: https://www.arb-silva.de/silva-license-information/#c2403