June 2021 - FROGS News
A new FROGS version is available:FROGS v3.2.3 has just been uploaded on the github:
For an easy installation there are :
Conda : https://anaconda.org/bioconda/frogs
Toolshed : https://toolshed.g2.bx.psu.edu/repository?repository_id=11a27cab761b5c8c&changeset_revision=834843ebe569
This new version is available on the Genotoul Bioinfo https://vm-galaxy-prod.toulouse.inra.fr/galaxy (INRAE Toulouse) and Migale https://migale.inrae.fr/galaxy (INRAE Jouy-en-Josas) platform.
What has changed since the last version?
- Filters has been split into 2 new tools : FROGS OTU Filters and FROGS Affiliations Filters.
- FROGS OTU Filters filters OTU on presence/absence, abundances and contamination as Filters did. For contamination research, user may now use a personnal multifasta contaminant reference. Now, you can filter OTU on Arabidopsis thaliana chroloroplast sequence that it has been added to available contaminant reference list.
- FROGS Affiliation Filters deletes OTU or masks affiliation that do not respect affiliation metrics criteria, or belong to undesirable (partial) taxon.
- ITSx : add organism model option (beware, the more organisms you choose, the more you increase the calculation time)
- DESeq2 preprocess : Computes differential abundancy analysis
- DESeq2 visualisation : Creates table and plots to explore and illustrate the differential abundant OTUs
New documentation for using FROGS v3.2 on Galaxy is available:http://frogs.toulouse.inrae.fr/data_to_test_frogs/formation_documentations.tar.gz
A redesigned website:The website has a new look !
You will find, 16S benchmarking that correspond to the first publication of FROGS, and ITS benchmarking that we are currently publishing (see below).
Convincing results on ITS data processing:Before the publication of our last article, you can view the results of FROGS on the ITS data:
- On simulated data: http://frogs.toulouse.inrae.fr/ITS/frogs-its.html
- On biological data: http://frogs.toulouse.inrae.fr/ITS/frogs-its-meat.html
FROGS test data processing gives excellent recall rate and precision thanks to a smart ITS data management while accurately reconstructing the sequences as they are expected.
It can be used both on the command line and through a Galaxy interface, making it an easy access tool for everyone.
boxplot showing the overall precision (blue) and recall rate (orange) of each of the tools used to process test datasets (all datasets: 35, 115 and 515 species, ITS1 and ITS2, power law and uniform abundance distribution).
boxplot showing the overall precision (blue) and recall rate (orange) of each of the tools used to process meat datasets (all datasets: ITS1, ITS2 with ADN or PCR products).
A new SOP dedicated to ITS:This is the standard operation procedure for long and unmergeable reads from metabarcoding sequencing i.e. ITS, rpb2, D1-D2
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.
For Silva databases, we propose reduced version based on a pintail score threshold.
The pintail score indicates the quality of the sequence.
See https://www.arb-silva.de/documentation/faqs/ Section : "What do the green, yellow and orange quality bars tell me?" for a brief explanation
or http://aem.asm.org/content/71/12/7724.abstract , for the pintail score paper.
You need help to use FROGS, you are looking for training:Please contact firstname.lastname@example.org
April 2019 - FROGS News
FROGS v3.1FROGS v3.1 is available on github : https://github.com/geraldinepascal/FROGS/releases .
What has changed since the v. 3.0 :
- Tsv_to_Biom : manages the quotation marks that Excel adds when saving in TSV.
- Affiliation_postprocess :resolves bug when references are not in the troncated amplicon database.
- Removal in the FROGS Tree tool of the possibility to use a Pynast alignment as a model.
- (for admins) XML wrappers, images and loc file have been moved to another github repository FROGS-wrappers
Toolshed and Conda repository:(for admins): FROGS installation and updates are now easier thanks to the FROGS repositories in Toolshed Galaxy and CONDA.
https://anaconda.org/bioconda/frogs and https://toolshed.g2.bx.psu.edu/view/frogs/frogs_3_1_0/59bc96331073
New databases are available. Here is the complete list including the new features in green:
SILVA/ --> data related to the SILVA 16S database (https://www.arb-silva.de/download/arb-files/)silva_132_16S.tar.gz --> data related to the version 132
silva_132_16S_pintail50.tar.gz --> data related to the version 132, filtered on pintail score >=50
silva_132_16S_pintail80.tar.gz --> data related to the version 132, filtered on pintail score >= 80
silva_132_16S_pintail100.tar.gz -->data related to the version 132, filtered on pintail score = 100
silva_128_16S.tar.gz --> data related to the version 128
silva_128_16S_pintail50.tar.gz --> data related to the version 128, filtered on pintail score >= 50.
silva_128_16S_pintail80.tar.gz --> data related to the version 128, filtered on pintail score >= 80.
silva_128_16S_pintail100.tar.gz --> data related to the version 128, filtered on pintail score = 100.
silva_123_16S.tar.gz --> data related to the version 123
Greengenes/ --> data related to the greengenes database (http://greengenes.secondgenome.com/)greengenes_13_5.tar.gz --> data related to the version 13.5
DAIRYdb/ --> data related to the DAIRYdb database (16S rRNA gene sequences from dairy products, https://github.com/marcomeola/DAIRYdb)DAIRYdb_v1.1.2.tar.gz --> data related to the version 1.1.2
EZBioCloud/ --> data related to EZBioCloud database (https://www.ezbiocloud.net/resources/16s_download)EZBioCloud_052018.tar.gz --> release 05/2018
SILVA/ --> data related to the SILVA 18S database (https://www.arb-silva.de/download/arb-files/)silva_132_18S.tar.gz --> data related to the version 132 silva_128_18S.tar.gz --> data related to the version 128 silva_123_18S.tar.gz --> data related to the version 123 silva_119-1_18S.tar.gz --> data related to the version 119-1
PR2/ --> data related to the The Protist Ribosomal Reference (PR2) database v4.5 (https://github.com/vaulot/pr2_database/releases)pr2_gb203_4.5.tar.gz --> data related to the version v4.5 pr2_4.11.0 --> data related to the version v4.11.0
SILVA/ --> data related to the SILVA 23S database (https://www.arb-silva.de/download/arb-files/)silva_132_23S.tar.gz --> data related to the version 132 silva_128_23S.tar.gz --> data related to the version 128 silva_123_23S.tar.gz --> data related to the version 123
ITS/ - Unite only for now (https://unite.ut.ee/)Unite_s_7.1_20112016_ITS.tar.gz --> data related to UNITE 7.1 database Unite_Fungi_8.0_18112018.tar.gz --> data related to UNITE 8.0 database focused on fungal species Unite_Euka_8.0_18112018.tar.gz --> data related to UNITE 8.0 database for all eukaryote species
MiDas/ (Microbial Database for Activated Sludge : http://www.midasfieldguide.org/)MiDAS_S119_1.20.tar.gz --> data related to the MiDAS S119 1.20 database (based on Silva.119) MiDAS_S123_2.1.3.tar.gz --> data related to the MiDAS S123 2.1.3 database (based on Silva 123)
rpoB/ (for rpoB marker, not yet published, see rpoB/README.txt)rpoB_122017.tar.gz
RSyst_Diatom/ (for rbcL diatoms barcode :https://www6.inra.fr/r-syst_eng/Databases/R-Syst-diatom)RSyst_Diatom_7.tar.gz --> data related to the R-Syst::Diatom version 7 (http://184.108.40.206/new_rsyst_alg/)
PHYMYCO_DB/ (EF1 and 18S fungal DNA markers: http://phymycodb.genouest.org/)PHYMYCO-DB_2013.tar.gz --> data related to the curated version of 2013.
BOLD_COI-5P/ BOLD_COI-5P_022019 --> data related to BOLD database (http://v3.boldsystems.org)BOLD_COI-5P_1percentN_022019 --> data related to BOLD database (http://v3.boldsystems.org), with maximum 1% of N
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