Kaptive 3¶

Kaptive provides rapid, accurate in silico typing of bacterial surface polysaccharide loci (such as K capsule and O lipopolysaccharide antigens) from whole-genome assemblies.

Originally created for Klebsiella pneumoniae and Acinetobacter baumannii, Kaptive 3 represents a complete ground-up re-architecture with a modern Python API, faster alignment pipelines, and extensible locus databases.

Key Features¶

• Fast Alignment-Driven Typing: Replaces legacy BLAST workflows with minimap2 for orders-of-magnitude faster locus identification and gene extraction.
• Python API & CLI: Use Kaptive either from the command line or programmatically as a Python library in custom genomic surveillance pipelines.
• Phenotype Prediction: Infers structural serotypes from gene presence, truncation, and allelic variation.

Citation¶

Stanton TD, Hetland MAK, Löhr IH, Holt KE, Wyres KL. Fast and accurate in silico antigen typing with Kaptive 3. Microbial Genomics. 2025;11(6). DOI: 10.1099/mgen.0.001428

← Back to all Software

Comments