Virulence gene identification software tools | Whole-genome sequencing data analysis

Provides a method for virulence-based classification of Bacillus cereus group isolates and/or antimicrobial resistance gene detection using nucleotide sequencing data. BTyper is a computational tool to perform (i) virulence gene detection, (ii) MLST, (iii) panC clade typing, and (iv) rpoB allelic typing using Bacillus cereus group nucleotide sequencing data. This method can be used to genotype foodborne pathogens and can become more valuable from a risk assessment perspective.

Enables mass screening of contigs for virulence genes or antimicrobial resistance. Abricate includes eight pre-downloaded databases (Resfinder, CARD, ARG-ANNOT, NCBI ARRGD, EcOH, PlasmidFinder, VFDB and Ecoli_VF). This software identifies acquired resistance genes but does not find mutational resistance. Users can create their own database by using a FASTA file of nucleotide sequences.

Detects virulence genes included in routine typing, and assigns verocytotoxin (vtx) subtypes. The VirulenceFinder approach may be applied to typing and surveillance of other pathogens. This tool was made for automatic detection and extraction of Escherichia coli virulence genes from whole genome sequencing (WGS) data. User can submitted sequence data either as assembled genomes or raw reads from various sequencing technologies. It allows to select configuration for the organism of interest and to select percent identity threshold between the input and the best matching database gene.