The clc_quality_trim program is used to trim sequencing reads for low quality. The idea is to trim the reads at one or both ends so that only a region of high-quality bases are left. This is done by specifying a threshold value (using the `-c' option) for low-quality base calls. The default value is 20, which means that quality scores below 20 are marked as low quality. Since it is often not desirable to discard a high-quality region because of one isolated low-quality base, you can specify the fraction of low-quality bases allowed in a region using the `-b' option. The default value is 0.1 meaning that up to 10 % low-quality bases are allowed. The trim algorithm will then, for each read, find the longest region that fulfills these thresholds. Note that in some situations the full read will be discarded if no good quality regions can be found.
For paired data, two separate files are specified as output: one for the intact pairs (use the -p option for this output file) and one for the single reads whose mate was discarded during trimming (use the -o option for this output file).
There are other options to refine the quality trimming even more (see Options).