GenomonVirusChecker

Introduction

GenomonVirusChecker is a software for checking the viral sequences in fastq files.

Dependency

Python

Python (>= 2.7)

Software

blat

Install

git clone https://github.com/friend1ws/GenomonVirusChecker.git
cd GenomonVirusChecker
python setup.py build
python setup.py install

Preparation

First, you may need to prepare viral sequence reference files in fastq format. We have provided an example script for preparing the reference files.

cd resource
bash prepareVirus.sh

Also, you need to set up the path for blat before running the program.

Commands

genomon_virus_checker [-h] [--version] [-q minimum_match_thres] sequence1.fastq sequence2.fastq output_prefix virus_reference.fa