Virulence

Depends on the Assembly and quality workflow.

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).