Note: This topic is not applicable to BAM-based projects.
Upon completion of a de novo assembly, all of the single sequences that did not enter a contig are in the Unassembled Sequences window and can be viewed by selecting Sequence > Add. To add these sequences to the existing assembly, first adjust the parameters, and then click Assemble from the Unassembled Sequences window.
It may also be beneficial to start with a Minimum Match Percentage greater than 80 and then decrease it from there. (See Assembling parameters for more information.)