Metadata-Version: 2.1
Name: checkv
Version: 0.2.0
Summary: Assess the quality of metagenome-assembled viral genomes.
Home-page: https://bitbucket.org/berkeleylab/checkv
Author: Stephen Nayfach, Antonio Pedro Camargo, Simon Roux
License: Modified BSD
Description: ![](https://bitbucket.org/berkeleylab/checkv/raw/758a99a857ee874f273c7de326679dfdf7e38847/logo.png)
        
        Assessing the quality of metagenome-assembled viral genomes
        
        ## Installation
        
        There are two methods to install CheckV in your computer:
        
        - Using `conda`:
        
        ```bash
        conda install -c conda-forge -c bioconda checkv
        ```
        
        - Using `pip`:
        
        ```bash
        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:
        
        ```bash
        wget https://www.dropbox.com/s/xz8h7d1ycrf4fjf/checkv-db-v0.4.tar.gz
        tar -zxvf checkv-db-v0.4.tar.gz
        ```
        
        Update your environment:
        
        ```bash
        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:
        
        ```bash
        cd /path/to/checkv/test
        ```
        
        Identify flanking host regions on integrated prophages:
        
        ```bash
        checkv contamination test.fna checkv_out -t 16
        ```
        
        Estimate completeness for genome fragments:
        
        ```bash
        checkv completeness test.fna checkv_out -t 16
        ```
        
        Identify (possible) complete genomes with terminal repeats:
        
        ```bash
        checkv terminal_repeats test.fna checkv_out
        ```
        
        Summarize CheckV output & classify contigs into quality tiers:
        
        ```bash
        checkv quality_summary test.fna checkv_out
        ```
        
        
        
        
        
Keywords: bioinformatics,genomics,metagenomics,viromics
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.6
Description-Content-Type: text/markdown
