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Trim bases from both ends (Figure 3) allows user to keep only bases from a fixed start and end position of the reads. This is particularly useful if poor quality bases are observed on both ends  of the read. So instead of performing trim bases successively from the 5'- and 3'-end, the trim bases will only be performed once by trimming from both ends.

Trim bases based on quality score (Figure 4) is probably the most useful function to trim poor quality bases from the 5'- or 3'-ends of reads. This function allows dynamic trimming of bases depending on quality score. The trimming can be done from either 5'-end, 3'-end or both ends of the reads. The function evaluates each base from the end of the read and trims it away until the last base has a quality score greater than the specified threshold. For an extensive evaluation of read trimming effects on Illumina NGS data analysis, see Del Fabbro et. al. [1].

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1. Del Fabbro C, Scalabrin S, Moragante M, Giorgi FM. An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS ONE. 2013; 8(12): e85024.