- recipe virasign
Virasign is a viral taxonomic classification tool designed for nanopore sequencing data.
- Homepage:
- Documentation:
https://github.com/DaanJansen94/virasign/blob/main/README.md
- License:
GPL / GPL-3.0-or-later
- Recipe:
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:
on curl
on gzip
on minimap2
2.24.*on mmseqs2
on python
>=3.7,<3.14on samtools
>=1.17on seqtk
1.3.*
- 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 virasign
to add into an existing workspace instead, run:
pixi add virasign
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 virasign
Alternatively, to install into a new environment, run:
conda create -n envname virasign
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/virasign:<tag>
(see virasign/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/virasign/README.html)
