Welcome to the User Manual for the Reference Libraries
The reference libraries are an integral part of a suite of genome analysis tools that explore bacterial genomes.
Reference genomes are used in multiple processes within the Tools. The reference libraries are required for:
- identification of contamination in raw read data
- taxonomy determination
- phylogenetic analysis
The reference libraries are maxThree, maxOne and kraken2.
The suite of genome analysis tools 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).