#fastq_qual_trimmer ##What it does? It trims and filters Sanger encoded FASTQ files by quality, length and homopolymer count. ##Installation To install on Unix systems with git, type:

git clone https://github.com/ivars-silamikelis/fastq_qual_trimmer
cd fastq_qual_trimmer
make

binary file will appear that can be copied to /usr/local/bin/ or added to your $PATH

##Usage If you wish to trim by quality 25 both ends of reads in FASTQ file named test.fq, type

./fastq_qual_trimmer -i test.fq -q 25 

##Available options

Option	Argument	Description
-h	None	Prints help message
-i	Filename	Specifies input file
-q	Integer	Smallest allowed quality for nucleotides at read ends (default: 20)
-m	Integer	Smallest allowed mean read quality (default 0)
-l	Integer	Minimal allowed read length (default 1)
-H	Integer	Reads with homopolymers with specified length or higher will be filtered. Use 0 to switch off (default: 0)
-w	None	Use sliding window trimming. Trim nucleotides from both ends by calculating mean quality of nucleotides in the window (default: off)
-s	Integer	Specify size of sliding window (default: 5)
-b	None	Use sliding window and after that - default trimming approaches (default: off)