README.md

vClean

vClean is a fully automated command-line pipeline for assessing the multiple virus-derived contamination risk of environmental viral genomes.

Quickstart

Run the following commands to install vClean, download the database, and run the program. Replace </path/to/database>, <input_fasta_dir> and <output_dir> with the correct paths.

conda install -c conda-forge -c bioconda vclean
vclean download_database </path/to/database>
export VCLEANDB=</path/to/database>
vclean run <input_fasta_dir> <output_dir> [options]

Installation

You can install vClean as follows:

conda install -c conda-forge -c bioconda vclean python=3.9

Specify python version to be 3.9

Database installation

You have to download the databases. Please replace </path/to/database> with the desired path for downloading the database:

vclean download_database </path/to/database>

You'll need to use the -d flag or update the VCLEANDB environment variable to specify the database location:

export VCLEANDB=<path/to/database>

Run

You can simply run vClean as follows:

vclean run <input_fasta_dir> <output_dir> [OPTIONS]

Output files

In the output directory, two files are generated: Contamination_probability.tsv and feature_table.tsv. For sequences confirmed to be contaminated, new FASTA files containing only the longest contigs are stored in the purified_fasta directory within the output directory.