fastx_toolkit zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output Quality cut-off value Percent of bases in sequence that must have quality equal to / higher than cut-off value

**What it does** This tool filters reads based on quality scores. .. class:: infomark Using **percent = 100** requires all cycles of all reads to be at least the quality cut-off value. .. class:: infomark Using **percent = 50** requires the median quality of the cycles (in each read) to be at least the quality cut-off value. -------- Quality score distribution (of all cycles) is calculated for each read. If it is lower than the quality cut-off value - the read is discarded. **Example**:: @CSHL_4_FC042AGOOII:1:2:214:584 GACAATAAAC +CSHL_4_FC042AGOOII:1:2:214:584 30 30 30 30 30 30 30 30 20 10 Using **percent = 50** and **cut-off = 30** - This read will not be discarded (the median quality is higher than 30). Using **percent = 90** and **cut-off = 30** - This read will be discarded (90% of the cycles do no have quality equal to / higher than 30). Using **percent = 100** and **cut-off = 20** - This read will be discarded (not all cycles have quality equal to / higher than 20). ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/