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

Provides various next-generation sequencing (NGS) data analysis applications which are developed or optimized by Illumina, or from a growing ecosystem of third-party app providers. BAseSpace is a cloud platform that can be integrated with the industry’s leading sequencing platforms, without cumbersome or time consuming data transfer steps.

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.

Represents an interactive predictive genomics platform. SuperPhy incorporates knowledge from research on the pathogenesis and epidemiology of E. coli, as well as the tremendous amount of genotypic and phenotypic data that have previously been generated. This knowledge is used within SuperPhy to discover relationships among and about subgroups. It allows non-bioinformaticians to analyze new data against the background of other sequenced E. coli.

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.

Provides the workflow used to obtain whole-genome sequence data of 340 sequence type (ST) 772 Staphylococcus aureus isolates (the Bengal Bay clone). bengal-bay allows users to reproduce core analyses, including parameter settings, cluster resource configurations and versioned software distributions. The workflow implements Anaconda virtual environments, including software distributed in the Bioconda channel and is executable through Snakemake.