Kleborate v3 includes a rewrite of Kleborate. It aims to:
- Modularise the code for easier extensibility and maintenance
- Provide functionality for other species, e.g. Klebsiella oxytoca and Escherichia coli
- Replace the BLAST dependency with minimap2
Available modules for Kleborate v3:
- Basic contigs stats
- Mash-based species detection for Klebsiella and closely-related genera
- MLST on the KpSC aerobactin locus (iuc genes)
- MLST on the KpSC colibactin locus (clb genes)
- MLST on the KpSC Rmp locus (rmp genes)
- MLST on the KpSC salmochelin locus (iro genes)
- MLST on the KpSC yersiniabactin locus (ybt and irp genes)
- Chromosomal MLST for Escherichia coli using the Achtman scheme
- Chromosomal MLST for Escherichia coli using the Pasteur scheme
- Chromosomal MLST for the Klebsiella oxytoca species complex
- Chromosomal MLST for the Klebsiella pneumoniae species complex
- Virulence score (0-5) for the Klebsiella pneumoniae species complex, based on the results of the abst, cbst and ybst modules
- Genotyping acquired genes and mutations for the Klebsiella pneumoniae species complex
- Resistance score (0-3) for the Klebsiella pneumoniae species complex
- Resistance gene classes count
- Resistance genes count
- Wzi typing for K antigen prediction
- Module to call Kaptive for K (capsule) and O antigen (LPS) serotype prediction
For information on how to install, and run Kleborate v3 please visit the Docs.