taXaminer v0.7.3

New features:

• option for protein to gene ID mapping file
• feature for re-grouping of taxonomic assignments for plot labels
• filtering modul of gene/CDS/protein and contig sequences
• support of UniRefXX databases
• incorporation of non-coding genes
• creation of taxSun output
• adaptable coloring scheme
• adaptable sensitivity for DIAMOND search
• umap for dimensionality reduction

Updates:

• progress bars
• major runtime improvements

Fixes:

• stability of reading GFF files
  • duplicate gene IDs
  • Parent feature = gene ID for all subfeatures
  • duplicate IDs in gene subfeatures
• diamond installation with miniconda
• gene neighbor assessment

taXaminer v0.7.2

• added 3D display for PCA contribution of variables
• bug fix for matching user-given protein fasta file headers to gene ID
• added diamond hit statistics to contig summary
• bug fix for config parameters options 'False' parsed incorrectly
• fixed 'update_plots' function

taXaminer v0.7.1

• diamond sensitivity setting adjustable
• fixed contig assignment when all genes are unassigned
• non-coding genes skipped in gene neighbourhood assignment
• updated log messages

taXaminer v0.7.0

• taXaminer goes python:
  • R modules have been replaced by python versions
  • installation as python package using the directory path possible
• taxonomic assignment:
  • altered algorithm for taxonomic assignment
  • overview file of taxonomic assignment per contig added
  • Krona plot of taxonomic assignment is generated
• coverage data:
  • read mapping support has been removed
  • coverage information only accepted in BAM format
• misc output changes:
  • gene neighbour information added to output
  • contribution of variables added to interactive 3D scatter plot
  • altered output for PCA results