Trimming as a separate task can be done either manually or automatically.
In both instances, trimming of a sequence does not cause data to be deleted, instead both the manual and automatic trimming will put a "Trim" annotation on the trimmed parts as an indication to the assembly algorithm that this part of the data is to be ignored (see figure 18.4). This means that the effect of different trimming schemes can easily be explored without the loss of data. To remove existing trimming from a sequence, simply remove its trim annotation (see Adding and modifying annotations).
Note! If you wish to have the contamination removed completely, you should use the NGS trim tool (see Trimming).