Submitted by orue on
frogs 3.2 update

The last available release has been installed on migale server and on Galaxy instance.

Major changes have been made since version 3.1. Some options have changed, and new tools are now available (details below).

SOP for 16S and ITS data anlysis are available at http://frogs.toulouse.inra.fr/

FROGS v3.1 is always available but is no more recommended. Galaxy users, be careful to choose the appropriate tools (section labels are named FROGS 3.2 or FROGS 3.1)

 

v3.2.2 [2021-04]

Modifications

  • Preprocess: use maxdiffpct instead of maxdiffs in vsearch fastq_mergepairs command line, and recommand 2.17.0 version.
  • DESeq2 :
    • rename tool in DESeq2 visualisation (with s instead of z)
    • improve filter in datatable
    • change color
    • add padj threshold in MAplot
  • ITSx : add organims model option (it was restrict to Fungi, take care of increase computing time
  • OTU affiliation : sort blast affiliations in biom by taxonomy
  • Clusters stat : add precision in HTML
  • Remove chimera : add precision in HTML, and rename table columns names
  • Affiliation Filter : add precision in HTML
  • Various tools:
    • add taxonomic rank consistency between user declaration and input files (reference database, biom)
    • correct typo

Bug fixed

  • DESeq2 visualisation :
    • add intermediates_dir argument in Rscript command
    • debug pie charts color attribution
  • Normalisation : correct bug when calculating number of OTU by sample
  • ITSx : correct stderr scanning
  • Affiliation filter : correct bug in OTU filter by sample and by filter

v3.2.1 [2021-02-22]

Bug fixed

  • correct reversecomp function by taking into account S and W IUPAC nucleotides

v3.2 [2021-01-13]

Tools added:

  • DESeq2 preprocess : Compute differential abundancy analysis
  • DESeq2 visualization : Create table and plots to explore and illustrate the differential abundant OTUs
  • Filters has been splitted into to 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.
    • FROGS Affiliation Filters delete OTU or mask affiliation that do not respect affiliation metrics criteria, or affiliated to undesirable (partial) taxon.

Function added

  • Affiliation_postprocess : taxon-ignore option added, to ignore some taxon like "unknown species" during the aggreagation process. Multiple taxon may be provided as well as partial taxon, like "sp."
  • Preprocess : now accept input sequence file as Fasta format (format automatically detected) for already contiged input.
  • Affiliations_stat : check that the number of rank name correspond to the number of ranks in input biom file
  • FROGSSTAT Phyloseq import : check sample names consistency between sample metadata and input biom file
  • FROGS OTU Filters filters OTU on presence/absence, abundances and contamination as Filters did.

Bug fixed

  • Affiliation_postprocess : correctly compare de %coverage and the coverage threshold.
  • FROGSSTAT Structure : plot_heatmap now take into account ordination method and dissimilarity matrix
  • addAffiliation2biom : do not split partial description from blast reference ID
  • tsv_2_biom now keep initial OTU order (Cluster_1 is the most abundant one and Cluster_X the less abundant one)

Other improvements

  • All python scripts are now in python 3
  • FROGSSTAT Phyloseq and FROGSSTAT DESeq now generate notebook_html instead of classical HTML output file. This facilitates code maintenance.