Homopolymer trimming

Configuration for the homopolymer trimming step is shown in figure 28.12.

Image trimstephomo
Figure 28.12: Homopolymer trimming.

Homopolymer trimming takes place only if at least one read end type is selected. After selecting the read end(s) to trim, you can select the type of homopolymer stretches to be removed.

How it works

Trimming of each type of homopolymer at each read end is done in the same way.

Using polyG as an example:

The window then slides by one position, to cover 9 of the original bases and 1 additional base, and the steps decribed above are repeated.

This process continues until the sliding 10-base window contains fewer than 9 Gs. At that point, checking stops and all bases marked to be trimmed are removed.

Examples of the effects of trimming particular sequences: