Two major approaches to detect structural variants in an individual genome from next-generation sequencing data are <i>de novo</i> assembly and resequencing.
<p>In <i>de novo</i> assembly, the individual genome sequence is constructed by examining overlaps between reads. In resequencing approaches, reads from the individual genome are aligned to a closely related reference genome. Examination of the resulting alignments reveals differences between the individual genome and the reference genome.</p
