Wiki¶

Raw reads¶

Available on katiel@slurm.ilifu.ac.za:/scratch3/users/katiel/Clinton/

Analyses¶

Available on katiel@slurm.ilifu.ac.za:/scratch3/users/katiel/Clinton/

1. srst2 AMR profiling against the ARGAnnot DB (haven't found a VF DB for Serratia
2. Core SNPs (alignment) and WGS assembly (gene presence/absence matrix) using Tychus

R downstream analyes: AMR heatmap with phylogenetic tree constructed from core SNP data.