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README.md

Kleborate container

Main tool : Kleborate 2.3.2

Additional tools:

  • kaptive 2.0.6
  • ncbi-blast+ 2.9.0
  • mash 2.3
  • python 3.8.2
  • biopython 1.81

Full documentation: https://github.com/katholt/Kleborate/wiki

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

Example Usage

# run Kleborate on assembly supplied with Kleborate code
kleborate --resistance --kaptive --all \
        --assemblies /Kleborate/test/test_genomes/172.fasta.gz \
        --outfile /data/strain172-kleborate-test-out.tsv