If paired reads were sequenced with an insert size shorter than twice the read length then pairs may overlap with each other, in which case it can be useful merge to each pair into a single longer read. After setting up paired reads (see section 10.2.1 ), use Merge Paired Reads... from the Sequence menu to merge them.
This function uses BBMerge from the BBtools suite. For a detailed explanation of any BBMerge setting, hover the mouse over the setting, or click the help (question mark) button next to the custom options under More Options.
Alternatively, an experimental plugin for merging paired reads using FLASH is available from the Geneious website plugins page.