Output

Classification results

Final classification results can be found in results/<analysis_id>/crassus_results.tsv. This is a tabular file with each row representing a contig identified as candidate Crassvirales. Information below is provided for each of these contigs:

  • crassus_id: unique CrassUS identifier

  • contig: user contig identifier

  • sample: sample of the contig

  • length: length of the contig

  • len/taxa_len: relation between contig length and the average genome length of the deepest predicted Crassvirales taxa.

  • ref_taxa: deepest predicted Crassvirales taxa for the contig

  • DTR: Direct Terminal Repeats detected (True or False)

  • family: Predicted Crassvirales family, if any

  • subfamily: Predicted Crassvirales subfamily, if any

  • genus: Predicted Crassvirales genus, if any

  • species: Predicted Crassvirales species, if any

  • evidence_family: Signals supporting the family assignment

  • evidence_genus: Signals supporting the genus assignment

  • notes: warnings about the assignments

  • discard: True if there was not enough evidence to classify the contig at least at the family level.

Phylogenies for iToL

After inferring the phylogenies of the three marker genes, CrassUS generates annotation files suitable for iToL. To visualize the phylogeny, first upload the .nwk file under results/<analysis_id>/5_phylogenies/3_iToL, and once the tree is loaded, navigate to the Datasets > Upload annotation files section and upload the paired .txt file. You should be able to visualize the phylogeny with the reference sequences colored

Flowchart

Genome diagrams

If specified under the genomes_plot > generate_plots section of the config file, results/<analysis_id>/7_ANI/alignment_plots.pdf will be generated containing a figure for each candidate contig found by CrassUS. ORFs are depicted and colored according to their function. At the bottom the most similar reference genome is depicted as well as their alignment regions. Flowchart