kleborate

Tags: bacteria klebsiella amr virulence typing mlst serotype k-locus o-locus sample-scope

Genotyping and screening of Klebsiella genome assemblies.

Uses Kleborate to screen Klebsiella assemblies for Multi-Locus Sequence Type (MLST), species identity, antimicrobial resistance determinants, virulence plasmids (e.g., ybt, iuc, iro), and capsular serotype prediction (K and O loci).

Database Bundled

Kleborate bundles the required databases for species identification, MLST, and virulence/resistance gene detection.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

Outputs

record (
    meta: Record,
    tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Tab-delimited Kleborate results with species, MLST, virulence, and resistance predictions
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

Kleborate Parameters

Parameter	Type	Default	Description
--kleborate_preset	string	kpsc	Preset module to use for Kleborate (choices: kpsc, kosc, escherichia)
--kleborate_opts	string		Extra options in quotes for Kleborate

Used By

Subworkflows

• kleborate - Genotyping tool for Klebsiella pneumoniae and its related species complex.

Workflows

• kleborate - Comprehensive screening of Klebsiella genomes for virulence and resistance determinants.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• Kleborate
  Lam MMC, Wick RR, Watts, SC, Cerdeira LT, Wyres KL, Holt KE A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat Commun 12, 4188 (2021)

• Kaptive
  Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R, Thomson NR, Holt KE Identification of Klebsiella capsule synthesis loci from whole genome data. Microbial genomics 2(12) (2016)

Source

View source on GitHub

Version

KLEBORATE:
    - kleborate: 3.2.4