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 (see details in this paper).

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)

Contig stats

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. Therefore checking genome assembly quality metrics is important.

-m general__contig_stats

This module generates some basic assembly statistics and compares them to the species-specific thresholds from Qualibact to assess assembly quality (based on the species call reported by the module enterobacterales__species, which is a prerequisite). The QC_warnings column flags an assemblies that falls outside those specified thresholds, or if ambiguous bases (Ns) are detected in the sequence.

This module is included 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. read-based analysis, screen for contamination, etc).

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)
GC_content	G+C content of the assembly, reported as a percentage
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)