v4.1.0

v4.1.0 [2023-03]

Tools modified:

• FROGSFunc copynumber removed
• FROGSFunc placeseq : integrates FROGSFunc marker copynumber part
• FROGSFunc function : integrates FROGSFunc function copynumber part

Function added

• Preprocess: add a longread sequencer option to deal with longreads
• Itsx : add mutual exclusion between --region and --check-its-only
• Affiliation_filter : add a –-keep-blast-taxa option : Taxon list to keep in Blast affiliations. All others affiliations will be masks/delete.
• DESeq preprocess : adapt the tool to deal with function abundance table (output from FROGSFunc Function) in TSV format
• DESeq visualisation :
  • adapt the tool to functionnal abundance differential analysis
  • add Ipath3 visualisation functionnal abundance differential analysis
• FROGSFunc placeseq :
  • add %identity and %coverage between amplicon sequences and Picrust reference sequences.
  • add a line chart of NSTI values versus blasts %identity and %coverage values.
• FROGSFunc function :
  • in addition to NSTI, add filter on %identity and %coverage between amplicon sequences and Picrust reference sequences.
  • add a star plot to visualise the filter impact on taxonomies kept
  • parallelization of function abundance prediction on different function database (MetaCyc, KEGG, COG, ...), reducing the calculation time by more than half using all databases.

Bug fixed

• Remove_chimera : deal with empty sample to compute proportion of sequence kept in the report. Proportion is now set to NA.
• Affiliation_filter :
  • correctly find number of taxonomical rank
  • remove OTU without affiliation when using blast metrics filters