recipe kmc

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

Homepage:

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

Documentation:

https://github.com/refresh-bio/KMC/blob/v3.2.4/README.md

License:

GPL3 / GPL-3.0-or-later

Recipe:

/kmc/meta.yaml

Links:

biotools: kmc, doi: 10.1093/bioinformatics/btx304, doi: 10.1093/bioinformatics/btv022, doi: 10.1186/1471-2105-14-160

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

versions:

3.2.4-4,  3.2.4-3,  3.2.4-2,  3.2.4-1,  3.2.4-0,  3.2.1-3,  3.2.1-2,  3.2.1-1,  3.2.1-0, 

3.2.4-4,  3.2.4-3,  3.2.4-2,  3.2.4-1,  3.2.4-0,  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 libgcc:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends python:

<3.11

requirements:

additional platforms:

linux-aarch64,  osx-arm64

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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