A tool that trims reads based on quality score from a FastQ file. Requires FastQ input file and quality score conversion table. Optionally accepts user-specified quality score trim threshold, sliding window size, minimum read length, output file type, and output file name. If no input is specified for optional parameters, the following defaults are used:
- Threshold score: 20
- Window size: 4
- Minimum read length: none
- Output file type: FastQ
- Output file name: "output"
Download "QualityTrim.py" and "qscores.txt", and optionally the example input file provided.
Usage:
python QualityTrim.py -i <input fastq file> -s <qscore file> -t <threshold cutoff score> -w <sliding window size> -m <minimum read length> -f <output file type {fastq, fasta, both}> -o <output file name>
Example:
python QualityTrim.py -i input.fastq -s qscores.txt -f both -o python_example_output
Example output for the first 100 lines (25 sequences) of the example input file is included as "python_example_output.fastq" and "python_example_output.fasta"