FROGS News - October 2022

• FROGS News - October 2022
• 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?

FROGS v4.0.1 is available

FROGS v4.0.1 is can be downloaded on :
https://github.com/geraldinepascal/FROGS/releases
https://github.com/geraldinepascal/FROGS-wrappers/releases

For an easy installation there are :
: https://anaconda.org/bioconda/frogs
: https://toolshed.g2.bx.psu.edu/view/frogs/frogs/37e6f0c959bb

This new version is available among others on

What has changed since the last version?

Tools added:

PICRUSt2 is a software for predicting functional abundances based only on marker gene sequences. This tool is integrated as 4 FROGSFUNC tools :

• FROGSFUNC_step1_placeseqs : Places the OTUs into a reference phylogenetic tree.
• FROGSFUNC_step2_copynumbers : Predicts number of marker and function copy number in each OTU.
• FROGSFUNC_step3_functions : Calculates functions abundances in each sample.
• FROGSFUNC_step4_pathways : Calculates pathway abundances in each sample.

Modified tools

Normalisation tool :

• We added “Sampling by the number of sequences of the smallest sample” sampling method. This method automatically detects the sample with the smallest number of sequences, and samples all other samples with that number.

• If you chose “Select a number of reads” sampling method, you may or not activate “Remove samples” option. If enabled, samples with a total number of sequences less than the specified number will be removed from the abundance table. If disabled, samples will be kept in the analysis but with less than the specified number of sequences (the total number of sequences in the sample).
  

OTU_filter tool :

Two options for filtering OTUs on prevalence criteria are now available.

1. the OTU must be present in X samples
   

2. the OTU must be present in X samples forming the condition
   

Affiliation_stat tool :

In addition to the ability to create rarefaction curves on taxonomic ranks, it is now possible to create them on OTUs.

Remove_chimera tool :

We add “% Clusters kept” and “% Cluster abundance kept” in HTML chimera detection by sample table.

New documentations for using FROGS v4.0.1:

• To try FROGS on Galaxy server (documentation + datasets):
  http://genoweb.toulouse.inra.fr/~formation/15_FROGS/current/

• Tutorials are now availbale to use FROGS on Galaxy and in command line:
  http://frogs.toulouse.inrae.fr/html/tuto.html
  Come back to visit this page regularly, the tutorials will grow over the months.

New databases are available

http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/readme.txt, here are all the databases we have formatted (on demand) for RDPClassifier and NCBI Blast+
Please pay attention to the licence of the database and how to cite it.

You need help to use FROGS, you are looking for training:

Please contact frogs-support@inrae.fr

And/or visit:
for a webinar training: http://frogs.toulouse.inrae.fr/html/training.php
next session: 3^th to 6^th April 2023

for a presential training at Jouy-en-Josas:
https://migale.inrae.fr/trainings

Lucas Auer joined le team !
Reasearch engineer in biostatistics at INRAE at IAM (Tree-microbe interactions) lab in Nancy. Specialist in fungal meta-omics approaches in soils.

Who uses FROGS?

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