Prior to de novo assembly, it can sometimes be useful to error correct the data or to normalize coverage by discarding reads in regions of high coverage. This functionality is available using Error Correct & Normalize Reads... from the Sequence menu.
This function uses BBNorm from the BBtools suite, and it requires Java 7 or later in order to run. For a detailed explanation of any BBNorm setting, hover the mouse over the setting, or click the help (question mark) button next to the custom options under More Options. For more information, see the BBNorm page on SeqAnswers.