FROGS News

April 2019 - FROGS News

FROGS v3.1

FROGS v3.1 is available on github : https://github.com/geraldinepascal/FROGS/releases .
What has changed since the v. 3.0 :
  1. Tsv_to_Biom : manages the quotation marks that Excel adds when saving in TSV.
  2. Affiliation_postprocess :resolves bug when references are not in the troncated amplicon database.
  3. Removal in the FROGS Tree tool of the possibility to use a Pynast alignment as a model.
  4. (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:

16S

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

18S/

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

23S/

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://138.102.89.206/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 News

The 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 News

FROGS 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:
  1. The modification of the "Preprocess Tool"
    1. to take into account ITS reads which could have the particularity of having non-overlapping reads
    2. to take into account the overlapping reads of all types
    3. we added the VSEARCH software for merging reads
    4. loss of the " Expected amplicon size" parameter with the VSEARCH tool
    5. 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.
  2. A new graphic charter for HTML outputs
  3. A new "ITSx" tool that identifies and extracts ITS regions
  4. To affiliate ITS, a new sequence affiliation strategy has been implemented. Adding needleall software
  5. 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.
For more details on how the tools work, please refer to the FAQ on the FROGS website.

Please be particularly attentive to the “FROGS_combined” section.

April 2018 - FROGS News

The 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 News

In 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 News

The 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