- recipe panqc
A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses
- Homepage:
- License:
MIT / MIT
- Recipe:
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:
on colored
on mappy
2.26on mmh3
on networkx
on pandas
on python
on screed
on tqdm
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install panqc
to add into an existing workspace instead, run:
pixi add panqc
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install panqc
Alternatively, to install into a new environment, run:
conda create -n envname panqc
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/panqc:<tag>
(see panqc/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/panqc/README.html)
