Trimming as described in this section involves marking of low quality and/or vector sequence with a Trim annotation as shown in figure 33.4
). Such annotated regions are then ignored when using downstream analysis tools located in the same section of the Workbench toolbox, for example Assembly (see Assemble sequences
). The trimming described here annotates, but does not remove data, allowing you to explore the output of different trimming schemes easily.
Trimming as a separate task can be done manually or using a tool designed specifically for this task.
Figure 33.4: Trimming creates annotations on the regions that will be ignored in the assembly process.
Note! If you wish to remove regions that are trimmed, you should instead use the NGS trim tool (see Trimming).
When exporting sequences in fasta format, there is an option to remove the parts of the sequence covered by trim annotations.