recipe kleborate

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.

Homepage

https://github.com/katholt/Kleborate

License

GPL3 / GNU General Public License v3 or later (GPLv3+)

Recipe

/kleborate/meta.yaml

package kleborate

(downloads) docker_kleborate

Versions

0.3.0-0

Depends blast

>=2.2.31

Depends mash

Depends python

Requirements

Installation

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

conda install kleborate

and update with:

conda update kleborate

or use the docker container:

docker pull quay.io/biocontainers/kleborate:<tag>

(see kleborate/tags for valid values for <tag>)