General modules

Species detection

-m enterobacterales__species

This module will attempt to identify the species of each input assembly. It does this by comparing the assembly using Mash to a curated set of Klebsiella and other Enterobacteriaceae assemblies from NCBI, and reporting the species of the closest match.

Parameters

--enterobacterales__species_strong

Mash distance threshold for a strong species match (default: 0.02)

--enterobacterales__species_weak

Mash distance threshold for a weak species match (default: 0.04)

Outputs

Output of the species typing module is the following columns:

species	Species name (scientific name)
species_match	Strength of the species call indicated as strong (Mash distance ≤ 0.02) or weak (Mash distance of > 0.02 and ≤ 0.04, may be novel or hybrid species)

The quality and completeness of Kleborate results depends on the quality of the input genome assemblies. In general, you can expect good results from draft genomes assembled with tools like SPAdes from high-depth (>50x) Illumina data, however it is always possible that key genes subject to genotyping may be split across contigs, which can create problems for detecting and typing them accurately.

Contig stats

-m general__contig_stats

This module takes enterobacterales__species as a prerequisite and generates some basic assembly statistics to help users understand their typing results in the context of assembly quality, although we recommend users conduct more comprehensive QC themselves before typing genomes (e.g. screen for contamination, etc).

The module reports a standard set of assembly quality metrics (see Outputs below).

It will also flag in the QC_warnings column if an assembly size falls outside those specified in the species_specification.txt in the module directory, or if N50 <10 kbp or ambiguous bases (Ns) are detected in the sequence.

Outputs

Output of the contig stats module is the following columns:

contig_count	Number of contigs in the input assembly
N50	N50 calculated from the contig sizes
largest_contig	Size of largest contig (in bp)
total_size	Total assembly size (in bp)
ambiguous_bases	Detection of ambiguous bases (yes or no). If yes, the number of ambiguous bases is also provided in brackets.
QC_warnings	List of QC issues detected, including: ambiguous_bases(ambiguous bases detected) N50(N50 < 10 kbp), total_size (genome size falls outside expected range).