Kleborate v2.0.0

Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:

• MLST sequence type
• species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.)
• ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)
• virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)
• antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases
• K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive

This release (v2.0.0) is the one used for the manuscript describing Kleborate: Lam et al, 2021, Nature Communications.

For documentation and developments see https://github.com/katholt/Kleborate