CLC Genomics Workbench offers a number of ways to trim your sequence reads prior to assembly and mapping, including adapter trimming, quality trimming and length trimming. Note that different types of trimming are performed sequentially in the same order as they appear in the trim dialogs:
  1. Quality trimming based on quality scores
  2. Ambiguity trimming to trim off e.g. stretches of Ns
  3. Adapter trimming
  4. Base trim to remove a specified number of bases at either 3' or 5' end of the reads
  5. Length trimming to remove reads shorter or longer than a specified threshold
The result of the trim is a list of sequences that have passed the trim (referred to as the trimmed list below) and optionally a list of the sequences that have been discarded and a summary report (list of discarded sequences). The original data will be not be changed.

To start trimming:

        Toolbox | NGS Core Tools (Image ngsfolder) | Trim Sequences (Image trim)

This opens a dialog where you can add sequences or sequence lists. If you add several sequence lists, each list will be processed separately and you will get a a list of trimmed sequences for each input sequence list.

When the sequences are selected, click Next.