checkv 0.1.0

Assess the quality of metagenome-assembled viral genomes.

CheckV

Assessing the quality of metagenome-assembled viral genomes

Installation

There are two methods to install CheckV in your computer:

• Using conda:

conda install -c conda-forge -c bioconda checkv

• Using pip:

pip install checkv

If you decide to install CheckV via pip, make sure you also have the following external dependencies installed:

• BLAST+ (v2.5.0)
• DIAMOND (v0.9.30)
• HMMER (v3.3)
• Prodigal (v2.6.3)

CheckV database

Whichever method you choose to install CheckV you will need to download and extract database in order to use it:

wget https://www.dropbox.com/s/ysv382w01ee7y3t/checkv-db-v0.2.tar.gz
tar -zxvf checkv-db-v0.1.tar.gz

Update your environment:

export CHECKVDB=/path/to/checkv-db-v0.2

If you don't want to set the environmet variable, you can still use the database through the -d parameter.

Quick start

Navigate to CheckV test directory:

cd /path/to/checkv/test

Identify flanking host regions on integrated prophages:

checkv contamination test.fna checkv_out -t 16

Estimate completeness for genome fragments:

checkv completeness test.fna checkv_out -t 16

Identify (possible) complete genomes with terminal repeats:

checkv terminal_repeats test.fna checkv_out

Summarize CheckV output & classify contigs into quality tiers:

checkv quality_summary test.fna checkv_out