checkv 0.2.0

Assess the quality of metagenome-assembled viral genomes.

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)

The versions listed above were the ones that were properly tested. Different versions may also work.

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/xz8h7d1ycrf4fjf/checkv-db-v0.4.tar.gz
tar -zxvf checkv-db-v0.4.tar.gz

Update your environment:

export CHECKVDB=/path/to/checkv-db-v0.4

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

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