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README.md

Kleborate container

Main tool : Kleborate

⚠️ Note: Kleborate v3 is different from v2, please see here for the differences: https://kleborate.readthedocs.io/en/latest/index.html#changes-from-v2

Additional tools:

  • mash version 2.3
  • minimap2 version 2.28
  • kaptive version 3.0.0b6
  • biopython 1.84
  • dna-features-viewer 3.1.3
  • matplotlib 3.9.2
  • numpy 2.1.3

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

Description:

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

Included models

Kleborate has models for both Klebsiella and Escherichia species. The available presets and models are listed below.

Available presets: kpsc, kosc, escherichia

Available modules for Kleborate
-------------------------------
enterobacterales__species: Mash-based species detection for enterobacterales species

escherichia__mlst_achtman: chromosomal MLST for Escherichia coli using the Achtman scheme

escherichia__mlst_pasteur: chromosomal MLST for Escherichia coli using the Pasteur scheme

general__contig_stats: basic stats on the assembly's contigs

klebsiella__abst: MLST on the KpSC aerobactin locus (iuc genes)

klebsiella__cbst: MLST on the KpSC colibactin locus (clb genes)

klebsiella__rmpa2: typing for the rmpA2 gene

klebsiella__rmst: MLST on the KpSC Rmp locus (rmp genes)

klebsiella__smst: MLST on the KpSC salmochelin locus (iro genes)

klebsiella__ybst: MLST on the KpSC yersiniabactin locus (ybt and irp genes)

klebsiella_oxytoca_complex__mlst: chromosomal MLST for the Klebsiella oxytoca species complex

klebsiella_pneumo_complex__amr: Genotyping acquired genes and mutations for the Klebsiella pneumoniae species complex

klebsiella_pneumo_complex__kaptive: In silico serotyping of K and L locus for the Klebsiella pneumoniae species complex

klebsiella_pneumo_complex__mlst: chromosomal MLST for the Klebsiella pneumoniae species complex

klebsiella_pneumo_complex__resistance_class_count: Resistance gene classes count, excluding the Bla_chr class which is intrinsicresults of the
klebsiella_pneumo_complex__amr module

klebsiella_pneumo_complex__resistance_gene_count: Resistance genes counts, excluding the Bla class which is intrinsicresults of the
klebsiella_pneumo_complex__amr module

klebsiella_pneumo_complex__resistance_score: resistance score (0-3) for the Klebsiella pneumoniae species complex, based on the results of the
klebsiella_pneumo_complex__amr module

klebsiella_pneumo_complex__virulence_score: virulence score (0-5) for the Klebsiella pneumoniae species complex, based on the results of the abst, cbst
and ybst modules

klebsiella_pneumo_complex__wzi: WZI typing for K antigen prediction

Example Usage

kleborate -a sample.fasta -o outdir -p preset