#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) |