Welcome to the User Manual for Tool 1
This Tool is part of a suite of genome analysis tools that explore bacterial genomes. The suite includes:
| Application | Description |
|---|---|
| The Core | Genome assembly, taxonomic classification, phylogeny, annotation and mass screening. |
| Tool 1 | Mass screening with curated databases. |
| Tool 2 | Mass screening with genes you choose. |
| Tool 3 | Comparison of genomes, and phylogeny. |
| Tool 4 | Primer design: identification of unique stretches of DNA. |
They are built with the pipeline manager Nextflow, and operate within Singularity containers.
The suite was developed as part of a collaborative project between Volac International Ltd. and Cardiff University, partly funded by Innovate UK as part of a knowledge transfer partnership (KTP).
What is Tool 1 for?
Tool 1 screens genomes for antimicrobial resistance or virulence genes. It uses the latest version of curated and peer-reviewed databases.
For EFSA product registrations use Tool 1 to fetch the latest AMR report.
What does Tool 1 do?
Tool 1 downloads the most recent database version. The databases contain known antimicrobial resistance or virulence genes. Using the DNA sequences of these genes, and a local alignment search tool (blast) it detects acquired resistance genes in the genomes of your query strains.
Tool 1 then summarises the data and also makes a report summarising the run parameters including the date.