recipe virasign

Virasign is a viral taxonomic classification tool designed for nanopore sequencing data.

Homepage:

https://github.com/DaanJansen94/virasign

Documentation:

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

License:

GPL / GPL-3.0-or-later

Recipe:

/virasign/meta.yaml

Virasign (Viral Read ASSIGNment) is a viral taxonomic classification and reference selection tool for nanopore data. It maps long-read sequencing data (via minimap2) against viral databases (RVDB, RefSeq, or custom accessions) and performs taxonomic classification to identify viral species. Virasign generates comprehensive interactive HTML reports with filterable tables, charts and heatmaps. For each identified virus, Virasign also provides the closest reference sequence, mapped reads in FASTQ format, and BAM files which can be used to easily generate a consensus genome and visualize data (e.g., IGV). Virasign includes options to blind yourself from certain incidental findings (such as HIV, Hepatitis viruses, HTLV, EBV, CMV, HPV) when wanted, ensuring these findings do not appear in any output files, in line with consent guidelines and ethical research practices.

package virasign

versions:

0.0.2-0

depends curl:

depends gzip:

depends minimap2:

2.24.*

depends mmseqs2:

depends python:

>=3.7,<3.14

depends samtools:

>=1.17

depends seqtk:

1.3.*

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 virasign

and update with::

   mamba update virasign

To create a new environment, run:

mamba create --name myenvname virasign

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/virasign:<tag>

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

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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/virasign/README.html)