recipe recmpox

RecMpox flags potential recombination events in monkeypox consensus genomes.

Homepage:

https://github.com/DaanJansen94/RecMpox

Documentation:

https://github.com/DaanJansen94/RecMpox/blob/main/README.md

License:

GPL / GPL-3.0-or-later

Recipe:

/recmpox/meta.yaml

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 with Squirrel, finds diagnostic SNP positions where the references differ, then classifies each consensus genome at those positions. Genomes where both refs contribute at least 5% are flagged as potential recombinants. Recombination tracts and breakpoints are inferred along the genome.

package recmpox

(downloads) docker_recmpox

versions:

0.0.2-0,  0.0.1-0

depends minimap2:

depends python:

>=3.9

depends samtools:

depends squirrel:

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 recmpox

and update with::

   mamba update recmpox

To create a new environment, run:

mamba create --name myenvname recmpox

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/recmpox:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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