q2-viromics

A QIIME 2 Plugin for detecting viral genomes and assessing their quality.

Install development version of q2-viromics

Clone the repository:

git clone https://github.com/bokulich-lab/q2-viromics.git
cd q2-viromics

Then, run:

mamba create -n q2-viromics -c conda-forge -c bioconda -c https://packages.qiime2.org/qiime2/2024.10/metagenome/passed/ -c defaults q2cli q2-types checkv genomad pyhmmer

Activate q2-viromics environment

conda activate q2-viromics

Test it out!

Download sample input datasets

Fetch the geNomad database.

qiime viromics genomad-fetch-db --o-database genomad_db.qza --verbose

Run the geNomad analysis.

qiime viromics genomad-analysis --i-sequences input_sequences.qza --i-database genomad_db.qza --p-num-threads 8 --p-splits 8 --output-dir genomad_output --verbose

Fetch the checkV database.

qiime viromics checkv-fetch-db --o-database checkV_db.qza --verbose

Run the CheckV analysis.

qiime viromics checkv-analysis --i-sequences genomad_output/viruses.qza --i-database checkV_db.qza --p-num-threads 4 --output-dir checkV_output --verbose