recipe kmc

Tools for efficient k-mer counting and filtering of reads based on k-mer content.

Homepage:

https://github.com/refresh-bio/kmc

License:

GPL / GPL-3

Recipe:

/kmc/meta.yaml

KMC is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of DNA sequences. KMC tools allow performing various operations on k-mers sets.

package kmc

(downloads) docker_kmc

versions:
3.2.1-3,  3.2.1-2,  3.2.1-1,  3.2.1-0,  3.1.2rc1-0,  3.1.1-1,  3.1.1-0,  3.1.1rc1-2,  3.1.1rc1-1, 

3.2.1-3,  3.2.1-2,  3.2.1-1,  3.2.1-0,  3.1.2rc1-0,  3.1.1-1,  3.1.1-0,  3.1.1rc1-2,  3.1.1rc1-1,  3.1.1rc1-0,  3.1.0-0,  3.0.1-2,  3.0.1-1,  3.0.1-0,  3.0.0-3,  3.0.0-2,  3.0.0-1,  3.0.0-0,  2.3.0-3,  2.3.0-2,  2.3.0-1

depends bzip2:

>=1.0.8,<2.0a0

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 kmc

and update with::

   mamba update kmc

To create a new environment, run:

mamba create --name myenvname kmc

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/kmc:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/kmc/README.html)