Trim reads by quality

Description

Trims reads based on the quality values.

Details

This tool utilizes the PRINSEQ package. The filtering is calculated with PRIONSEQ options -trim_qual_left, -trim_qual_right, -trim_qual_type, -trim_qual_rule, -trim_qual_window,and -trim_qual_step

Sequences can be trimmed from either end using different rules applied to a sliding window. To stop at the first base that fails the rule defined, use a window size of 1. A bigger window size can trim sequences that might contain a high quality score in between low quality scores without stopping at the high quality score. To move the sliding window over all quality scores without missing any, the step size should be less or equal to the window size.

Output

The trimmed reads are saved to file called trimmed.fastq or trimmed.fasta. You can also print out a log file that contains information about the filtering task and statistics about how many reads were accepted and rejected.

Reference

This tool is based on the PRINSEQ package.