recipe kwip

kWIP implements a de novo, alignment free measure of sample genetic dissimilarity

Homepage:

https://github.com/kdmurray91/kWIP

License:

GNU General Public License version 3

Recipe:

/kwip/meta.yaml

Links:

biotools: kWIP, doi: https://doi.org/10.1371/journal.pcbi.1005727

package kwip

(downloads) docker_kwip

versions:

0.2.0-6,  0.2.0-5,  0.2.0-4,  0.2.0-3,  0.2.0-2,  0.2.0-1,  0.2.0-0

depends khmer:

depends libcxx:

>=15.0.7

depends libzlib:

>=1.2.13,<1.3.0a0

depends zlib:

requirements:

Installation

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 kwip

and update with::

   mamba update kwip

To create a new environment, run:

mamba create --name myenvname kwip

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 quay.io/biocontainers/kwip:<tag>

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

Notes

The k-mer Weighted Inner Product (kWIP) implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any reference genome, and without assembling one.

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