Welcome to the User Manual for Tool 3
This Tool is part of a suite of genome analysis tools that explore bacterial genomes. The suite includes:
| Application | Description |
|---|---|
| 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 3 for?
Tool 3 compares the gene make up between strains.
You might want to discover which genes are unique to a particular strain, or which strains are most closely related.
What does Tool 3 do?
Tool 3 compares the genomes of two or more bacterial strains. It looks at their annotated genomes and reports the presence or absence of every gene, for all strains.
For example, Tool 3 reports which genes are present in every strain; these are the core genes. Also, which genes are unique to a strain.
Additionally, Tool 3 draws a tree based on this comparison.