Assess the quality of metagenome-assembled viral genomes.
Project description
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.