- recipe virprof
Virus Identification, Quantification and Genome Recovery from RNA-Seq NGS data
- Homepage:
- License:
GPLv3
- Recipe:
VirProf is a dual RNA-seq analysis pipeline integrating host expression profile generation with virus identification, quantification, and genome recovery from host tissue RNA sequencing data. VirProf combines an unguided metagenomic assembly workflow with interleaved host read depletion followed by BLAST based binning, scaffolding and classification. Application of VirProf to poly-A selected RNA-seq data from nasal swabs with respiratory virus qPCR data, revealed that VirProf was able to a) quantify a range of viral infections at detection limits and precision comparable to qPCR and b) recover complete, accurate viral genomes suitable for phylogenetic analysis.
- package virprof¶
- Versions:
0.9.2-0- Depends:
on biopython
on click
on graph-tool-base
>=2.34on networkx
>=2.0on python
>=3.10,<3.12on requests
on tqdm
on ymp
>=0.3.2,<0.4
- 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 virprof
to add into an existing workspace instead, run:
pixi add virprof
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 virprof
Alternatively, to install into a new environment, run:
conda create -n envname virprof
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/virprof:<tag>
(see virprof/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/virprof/README.html)
