kleborate 3.0.0

Kleborate: a tool for typing and screening pathogen genome assemblies

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, based on the results of the kpsc_amr module
• 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.