recipe ectyper

ECtyper is a python program for serotyping E. coli genomes



Apache 2



package ectyper

(downloads) docker_ectyper



depends bcftools:


depends biopython:


depends blast:


depends bowtie2:


depends mash:


depends pandas:


depends pytest:


depends python:


depends requests:


depends samtools:


depends seqtk:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install ectyper

and update with::

   mamba update ectyper

To create a new environment, run:

mamba create --name myenvname ectyper

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `ectyper/tags`_ for valid values for ``<tag>``)

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