Homopolymer trimming

Configuration for the homopolymer trimming step is shown in figure 25.12.

Image trimstephomo
Figure 25.12: Trimming homopolymer.

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: A window of 10 nucleotides at the end of the read is initially checked. If fewer than 9 bases are Gs, then checking stops and no bases are trimmed. If at least 9 bases are Gs, then this stretch of 10 bases will later be trimmed away. The window then slides by one position, to cover 9 of the original bases and 1 additional base. If at least 9 of these 10 bases are Gs, then this stretch will be marked for trimming. 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: