Pathogen outbreak study - Pseudomonas single isolate WGS

A nextflow pipeline, Tychus, was identified for use with this project.

To do:¶

• Convert pipeline docker images to Singularity images for use on the UCT cluster/ ILIFU
• Adapt pipeline config files to successfully run on the relevant cluster
• Identify suitable reference genome for use with the 'alignment module' (fasta formatted)
• Specify antmicrobial resistance database for use with the 'alignment module' (fasta formatted)
• Specify virulence database for use with the 'alignment module' (fasta formatted)
• Specify plasmid database for use with the 'alignment module' (fasta formatted)