recipe wgfast

The whole genome focused array SNP typing (WG-FAST) pipeline



GPL / GPL v3



package wgfast

(downloads) docker_wgfast



depends bbmap:

depends biopython:

depends bwa:

depends click:

depends dendropy:

depends ete3:

depends logbook:

depends mash:

depends nasp:

depends ncbitk:

depends pandas:

depends pathos:

depends picard:

depends python:


depends qt:

depends raxml:

depends retrying:

depends samtools:

depends snakemake:




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 wgfast

and update with::

   mamba update wgfast

To create a new environment, run:

mamba create --name myenvname wgfast

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 `wgfast/tags`_ for valid values for ``<tag>``)

Download stats