Installation

Dependencies

Kleborate requires the following software and libraries to be installed and available in your path:

• Python v3.9 or later

• Biopython v1.75 or later

• Mash v2.0 or later

• Minimap2

• Kaptive

• DNA Features Viewer

• ectyper

• stxtyper

• ncbi-amrfinderplus

• EzClermont

Install Kleborate

Create a conda environment and install Kleborate dependancies:

conda create -n klebsiella_analysis -c bioconda python=3.9 minimap2 mash ezclermont ectyper stxtyper ncbi-amrfinderplus -y

Activate the conda environment and install kleborate using pip:

conda activate klebsiella_analysis

pip install kleborate

Or Bioconda:

conda install -c bioconda kleborate

Download the AMRFinder database:

amrfinder -u

Test installation:

wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/813/595/GCF_002813595.1_ASM281359v1/GCF_002813595.1_ASM281359v1_genomic.fna.gz
kleborate -a GCF_002813595.1_ASM281359v1_genomic.fna.gz -o kleborate_test -p kpsc