- recipe recmpox
RecMpox flags potential recombination events in monkeypox consensus genomes.
- Homepage:
- Documentation:
- License:
MIT / MIT
- Recipe:
RecMpox is a command-line tool that flags potential recombination events in monkeypox viruses. It identifies recombination tract breakpoints within your own provided consensus genomes. It does not confirm recombination; it flags genomes that may be recombinant for further investigation. RecMpox takes two references (e.g. Clade Ia vs Ib, or IIa vs IIb), aligns them, finds diagnostic sites, and classifies each genome along the alignment to infer recombination tracts and breakpoints. Optionally, RecMpox can build a phylogeny of the inferred tract sequences alongside outbreak references, to help confirm true recombination and reduce false positives caused by ancestral population structure.
- package recmpox¶
- Versions:
0.0.5-0,0.0.4-0,0.0.3-0,0.0.2-0,0.0.1-0- Depends:
on bioconductor-ggtree
on iqtree
2.4.0.*on minimap2
on python
>=3.9on r-ape
on r-base
on r-ggplot2
on r-phytools
on samtools
on squirrel
- 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 recmpox
to add into an existing workspace instead, run:
pixi add recmpox
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 recmpox
Alternatively, to install into a new environment, run:
conda create -n envname recmpox
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/recmpox:<tag>
(see recmpox/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/recmpox/README.html)
