Genotyping
What this exercise tests
You are given bacterial genome assemblies. The result sheet asks for consistent species, sequence type, capsule and O-antigen calls, plus selected resistance determinants.
The worked route uses Kleborate, which is designed for the Klebsiella pneumoniae species complex.
Install Kleborate
Use a separate Conda environment:
conda create -n kleborate -c conda-forge -c bioconda \
--strict-channel-priority kleborate
conda activate kleborate
amrfinder -u
kleborate --version
kleborate --list_modules
See installing bioinformatics tools for general environment guidance.
Check the assemblies
Confirm that every file contains sequence and that identifiers are unique:
grep -H -m 1 '^>' input/*.fasta
ls -lh input/*.fasta
Very small, fragmented or contaminated assemblies can produce missing or multiple locus calls.
Run the KpSC preset
kleborate \
-a input/*.fasta \
-o kleborate_results \
-p kpsc \
--trim_headers
Kleborate accepts .fasta and .fasta.gz inputs. The KpSC preset reports
species, MLST, virulence, resistance and K/O locus information. Record the
Kleborate and database versions.
Interpret the output
Review warnings and confidence fields before transferring values:
st: MLST sequence type;k_locus: K-locus designation;capsule_type: capsule interpretation associated with the K locus;wzi: reported wzi allele;o_locus: O-antigen locus;o_type: O-antigen serotype interpretation;bla_carb: detected carbapenemase genes; andspecies: organism classification supported by the analysis.
The locus designation and inferred serotype are related but are not interchangeable. Keep missing, novel and low-confidence calls explicit.
Normalise the result sheet
Use the exact sample identifier and column names supplied by the exercise. Preserve allele and locus nomenclature. When more than one resistance determinant is present, use the requested separator and place explanations in a notes field rather than inside a controlled-value column.
Common problems
No ST call: Investigate missing or fragmented housekeeping loci, poor assembly quality or the wrong scheme.
Multiple alleles: Review contamination and mixed-sample evidence.
Unexpected species: Confirm the input and do not force the KpSC preset onto an unrelated organism.
Different calls between runs: Check Kleborate, Kaptive and AMRFinder database versions.