This repository contains a python script to create a simple diagnostic plot of read quality from input .fastq files. The data/ folder includes two example data files, with 1000 reads for forward and reverse, respectively (source: https://www.ncbi.nlm.nih.gov/sra/SRR622461).

To run the script you'll need python installed. An installation of Anaconda 3.x is recommended:

https://www.anaconda.com/download/

The code requires the biopython and matplotlib modules:

pip install biopython matplotlib

From the terminal use the following command to generate the read quality diagnostic plot:

python qcheck.py data/SRR622461_2.fastq data/SRR622461_2.fastq