FROGS News - April 2019



FROGS v3.1 is available

FROGS v3.1 is available on github : https://github.com/geraldinepascal/FROGS/releases .



What has changed since thev. 3.0?

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 bold

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




A work by FROGS team