Filtering / Filter out low quality reads


Given a FASTQ file, this tool filters out reads based on quality scores.



The quality value of every base in the read is compared to the quality value cut-off, and the percentage of bases having a quality score equal or higher than the cut-off value is calculated. If the percentage is not sufficient, the read is discarded. For example, if you set the percentage to 100, the quality value in every position must be equal or higher than the cut-off.


A FASTQ file where all the reads satisfy the quality criteria selected. In addition a log file is produced, telling how many reads the input file contained and what percentage of them were discarded as being low quality.


This tool is based on the FASTQ Quality Filter tool of the FASTX package.