recipe panqc

A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses

Homepage:

https://github.com/maxgmarin/panqc

License:

MIT / MIT

Recipe:

/panqc/meta.yaml

panqc is a pan-genome quality control toolkit that evaluates and corrects for nucleotide redundancy in pan-genome analyses. The panqc Nucleotide Redundancy Correction (NRC) pipeline adjusts for redundancy at the DNA level within pan-genome estimates by comparing genes classified as absent at the amino acid level against their corresponding assemblies at the nucleotide level and by clustering genes using k-mer based nucleotide similarity metrics.

package panqc

versions:

0.0.4-0

depends colored:

depends mappy:

2.26

depends mmh3:

depends networkx:

depends pandas:

depends python:

depends screed:

depends tqdm:

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 panqc

and update with::

   mamba update panqc

To create a new environment, run:

mamba create --name myenvname panqc

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/panqc:<tag>

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

Download stats

Link to this page

Render an 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/panqc/README.html)