recipe kcftools

Rapid method to screen for introgression using k-mer counting

Homepage:

https://github.com/sivasubramanics/kcftools

License:

GPL / GPL-3.0-only

Recipe:

/kcftools/meta.yaml

KCFTOOLS is a Java-based tool designed to identify genomic variations by analyzing k-mer counts between reference and query sequences. The tool leverages k-mer counting databases, such as those generated by KMC, to perform a variety of analyses, including variation detection, IBS window identification, and genotype matrix generation.

package kcftools

(downloads) docker_kcftools

versions:

0.1.0-0,  0.0.1-0

depends kmc:

>=3.2.0

depends openjdk:

17.*

depends python:

depends r-dplyr:

depends r-ggforce:

depends r-ggh4x:

depends r-ggplot2:

depends r-optparse:

depends r-svglite:

requirements:

additional platforms:

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 kcftools

and update with::

   mamba update kcftools

To create a new environment, run:

mamba create --name myenvname kcftools

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/kcftools:<tag>

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

Download stats

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/kcftools/README.html)