kleborate
Tags: klebsiella pneumoniae genotyping virulence capsule sample-scope
Genotyping tool for Klebsiella pneumoniae and its related species complex.
This subworkflow performs comprehensive genotyping of Klebsiella pneumoniae and related species using Kleborate. The tool identifies capsular (K) and O-antigen (L) loci, virulence factors, and acquired antimicrobial resistance genes, providing a detailed genotype for surveillance and epidemiological studies.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembly files in FASTA format for Klebsiella genotyping |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
tsv | Tab-delimited Kleborate results with species, MLST, virulence, and resistance predictions |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- kleborate - Genotyping and screening of Klebsiella genome assemblies.
Used By
This subworkflow is used by the following 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)