q2-virsorter2

A QIIME 2 Plugin for detection and analysis of viral genomes using VirSorter 2.

Installation

q2-virsorter2 can be installed into an existing QIIME 2 conda environment. The plugin should be compatible with the metagenome, pathogenome, and amplicon QIIME 2 distributions.

conda activate <environment name>

mamba install -c conda-forge -c bioconda -c defaults prodigal pyhmmer screed virsorter=2

pip install git+https://github.com/bokulich-lab/q2-virsorter2.git

qiime dev refresh-cache

Usage

Start by downloading sample input datasets.

Fetch the VirSorter database:

qiime virsorter2 fetch-db --o-database db.qza --verbose

Run the CheckV analysis:

qiime virsorter2 run --i-database db.qza --i-sequences input_sequences.qza --output-dir results/ --verbose