Virulence

Depends on the Assembly and quality workflow.

_images/virulence.svg

Steps to identify virulence factors

After the annotation of the genome, virulence factors are search by two different ways:

  • Factors longer than 50 amino acids are search by blastp over the proteome annotated by prokka
  • Factors shorter than 50 amino acids are search by tblastn directly over the contigs of the assembly

Parameters

  • virulence_factors: file with list of uniprot accession of virulence factors. An example is available in the folder data/staph/db/
Virulence data example
gene uniprot_accession description
hla P09616 Alpha-hemolysin
hld P0C1V1 Delta-hemolysin
hlgA P0A074 Gamma-hemolysin component A
hlgB P0A077 Gamma-hemolysin component B
  • virulence_percentage_identity_cutoff: amino acid identity cut off for considering a match
  • virulence_coverage_cutoff: coverage cut off for considering a match

Deliverables

  • virulence_summary.xlsx: summary of virulence proteins found in every samples (one per sheet).