kleborate

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A tool to screen Klebiella genome assembiles for: MLST sequence type, species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.), ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2), antimicrobial resistance genes, including quinolone resistance SNPs and colistin resistance truncations, and K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive.

Home https://github.com/katholt/Kleborate
Versions 0.3.0
License GNU General Public License v3 or later (GPLv3+)
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/kleborate

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install kleborate

and update with:

conda update kleborate

docker

A Docker container is available at https://quay.io/repository/biocontainers/kleborate.