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For Trim adapters, more than one adapter sequences can be specified at once. When multiple adapters are provided, all adapters are evaluated based on how many bases it overlaps the read as well as the error rate. Adapters which have a lower number of overlapped nucleotides or high error rates are removed from consideration.

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There are cases when the Trim adapters function does not work properly, for example: the existence of N's base in the read, etc. Therefore, there are advanced options which allows user to configure how the matching is done to trim adapter sequence. The advanced options dialog box is shown in Figure 8.

The first section of advanced options is the Adapter options. This is used to configure how the matching between the adapter sequence and the read will be performed. This includes the maximum error rate allowed, the number of matched times, minimum length of overlapped bases, allowing Ns (ambiguous base) in adapter and whether N will be treated as wildcards. User can roll-over mouse cursor to the info button to get more information of each parameter.

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