Major version v5.0.0

v5.0.0 [2024-06]

Tool added

• FROGS denoising: new tools replacing FROGS preprocess and FROGS clustering, allowing to perform the preprocess step and to chose between swarm and dada2 to produce ASVs.

Tools removed

• FROGS preprocess: its functionality is integrated in the new FROGS denoising tool
• FROGS clustering: its functionality is integrated in the new FROGS denoising tool

Global changes

• remove short version of parameters and standardization of parameter names
• add version and tool name in HTML reports
• add subject length information (slen) and related perc_subject_coverage in BIOM metadata for each affiliation
• remove and rename remaining tools/code with OTU term
• possibility to swith color theme in HTML reports

Functions added

• FROGS denoising:
  • add dada2 tool for Illumina paired-end data and PacBio long-reads data
  • add the possibility to perform a dereplication only instead of a clustering or denoising process
  • FROGS cluster stats tool integrated automatically in the HTML report
• FROGS demultiplex:
  • speed-up the way to check if file is gzipped
• FROGS taxonomic affiliation:
  • FROGS affiliation stats tool integrated automatically in the HTML report
  • Add subject length in BIOM
• FROGS remove chimera:
  • No more possibility to give a count matrix as input file
  • FROGS cluster stats tool integrated automatically in the HTML report
• FROGS itsx
  • FROGS cluster stats tool integrated automatically in the HTML report
• FROGS cluster stats
  • Hierarchical clustering no more done by default (option --hierarchical-clustering added)
• FROGS cluster filters
  • FROGS cluster stats tool integrated automatically in the HTML report
• FROGS phyloseq structure: use the same colors for samples in all ordination plots

Bugs fixed

• Standardization of empty affiliations in BIOM files (empty list instead of None)
  • impacts FROGS affiliation filters, FROGS biom to tsv, FROGS tsv to biom, FROGS cluster filters, FROGS taxnomic affiliation, libexec/biomTools.py
• Phyloseq import and DESeq preprocess: allow files beginning with digits
• Phyloseq import: remove empty samples and gives the information in the HTML report
• DESeq preprocess: check samples names consistency between function abundance tsv file and sample_metadata
• DESeq visualization
  • remove empty samples and taxa before plotting the heatmap
  • correct heatmap where there is only one ASV or Function differentially expressed
  • correct ipath3 associated color (higher = darker) and reduce width difference
  • correct associated color of LFC>0 or LFC<0 in ipath3 images
• libexec/launch_hsp.py: correct path for tmp files
• ASV without affiliation is deleted if a threshold on a blast metric is set in affiliation_filters.py
• Affiliation_filters: Error message and exit if an ASV with a taxonomy has missing metrics (no data) because of a manual update
• FROGSfunc functions: correction of the location of temporary files