FQTool

Tool to parse and filter FASTQ files


Keywords
fastq, read, bioinformatics, parser, fastq-files, fastq-format
License
GPL-3.0
Install
pip install FQTool==1.4

Documentation

FQTool

Introduction

This lightweight tool, written in Python, is designed to allow a simple -yet powerful- way to manipulate FASTQ files. The purpose of this tool is to filter those reads, taken from one or more FASTQ files, that satisfy all the constrains selected when running the tool. Some simple flags are used to set the constraints.

Installation

We decided to publish the package on PyPI to make the process of installing and upgrading FQTool easier for anyone. You need to have pip3 installed.

Just type sudo -H pip3 install fqtool in your terminal and you're ready to go! Check the examples and the flags to understand how to use FQTool.

Which flags are available?

fqtool -h   prints all the flags supported by FQParse. Here's the list:

  • -i, --input-filenames filename1 [filename2 filename3 ...]

    • Input file name(s). Usually in the form *.fastq, *.fq
  • -l, --length length

    • Minimum length of the reads' substrings to be extracted.
  • -q, --probability-of-correctness quality

    • Minimum probabilty of correctness of the reads to be extracted. Ranges between 0 and 1. You can also write the Phread Quality Value directly (e.g. 35)
  • -f, --ascii-conversion-function function

    • Function to be used to switch bewteen ASCII and Phred Value.Choose between: S = Sanger, X = Solexa, I = Illumina 1.3+, J = Illumina 1.5+, L = Illumina 1.8+. Default = L
  • -a, --accuracy accuracy

    • The average probability of correctness of the reads must be at least this value. If it is not, the read will be ignored. Default = 0
  • -v, --version

    • Shows the program version and exits
  • -h, --help

    • List of the flags you can use with FQTool

Examples

Some examples showing how to use FQTool can be found in the Examples directory. All the FASTQ files in that folder are taken from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/

Documentation

In this repository you will find a Doxyfile. Just type doxygen Doxyfile in a terminal to generate the project's documentation. You need to have doxygen installed.