- recipe mvip
MVP v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes and isolate genomes.
- Homepage:
- License:
GNU GENERAL PUBLIC LICENSE
- Recipe:
- package mvip¶
- Versions:
1.1.5-1,1.1.5-0,1.1.4-0,1.1.3-0,1.1.2-0,1.1.1-0,1.1.0-1,1.1.0-0,1.0.0-0- Depends:
on bowtie2
on checkv
on coverm
on dos2unix
on fasttree
on flit
on genomad
1.7.4on importlib_resources
on mafft
on minimap2
on mmseqs2
on numpy
1.23on pandas
on parallel
on python
>=3.7on rpy2
on samtools
on scikit-learn
0.23on seqtk
on table2asn
on taxopy
on tqdm
on trimal
on vrhyme
- 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 mvip
to add into an existing workspace instead, run:
pixi add mvip
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 mvip
Alternatively, to install into a new environment, run:
conda create -n envname mvip
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/mvip:<tag>
(see mvip/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/mvip/README.html)
