recipe virprof

Virus Identification, Quantification and Genome Recovery from RNA-Seq NGS data

Homepage:

https://github.com/seiboldlab/virprof

License:

GPLv3

Recipe:

/virprof/meta.yaml

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 biopython:

depends click:

depends graph-tool-base:

>=2.34

depends networkx:

>=2.0

depends python:

>=3.10,<3.12

depends requests:

depends tqdm:

depends ymp:

>=0.3.2,<0.4

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 virprof

and update with::

   mamba update virprof

To create a new environment, run:

mamba create --name myenvname virprof

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/virprof:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/virprof/README.html)