Metadata-Version: 2.4
Name: q2-viromics
Version: 2026.7.0.dev0
Summary: A QIIME 2 plugin for the identification and analysis of viral sequences.
Author-email: Christos Matzoros <christosmatzoros@gmail.com>
License: BSD 3-Clause License
        
        Copyright (c) 2024, Bokulich Lab.
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Project-URL: Homepage, https://github.com/bokulich-lab/q2-viromics
Project-URL: Repository, https://github.com/bokulich-lab/q2-viromics
Description-Content-Type: text/markdown
License-File: LICENSE
Dynamic: license-file

# q2-viromics

A [QIIME 2](https://qiime2.org) Plugin for detecting viral genomes and assessing their quality.

## Installation
_q2-viromics_ is available as part of the QIIME 2 pathogenome distribution. For installation and usage instructions please consult the official [QIIME 2 documentation](https://docs.qiime2.org). 


## Usage
Start by downloading sample input [datasets](https://polybox.ethz.ch/index.php/s/9jlQ4oyDWvWyvpB).

Fetch the checkV database:
```bash
qiime viromics checkv-fetch-db --o-database checkV_db.qza --verbose
```

Run the CheckV analysis:
```bash
qiime viromics checkv-analysis --i-sequences input_sequences.qza --i-database checkV_db.qza --p-num-threads 4 --output-dir checkV_output --verbose
```
