mean qual

mean-qual

Description

Script calculates mean quality of reads in fastq file(s) (*.fastq(.gz) or *.fq(.gz)).

Dependencies

The script is written in Python, so you need Python interpreter (version 3.X) to use it. Here you can download Python.

Explanation of output file

mean-qual writes it's output to tab-separated file ./mean-qual_result.tsv. In this file, nubmer of reads, mean quality and accuracy are written.

Options

-h (--help): print help message;

-v (--version): print version;

-o (--outfile): output file. Default: './mean-qual_result.tsv'.

-p (--phred-offset): Phred offset (33 of 64). Default: 33.

Usage

python3 mean-qual.py first.fastq second.fastq.gz third.fq.gz

Following command will process all *.fastq(.gz) and *.fq(.gz) files in the working directory:

python3 mean-qual.py