 time complexity of O(<var>n</var><sup>2</sup>); using a hash this can be reduced significantly). Referring to the comparison drawn to shredded books in the introduction: while for mapping assemblies one would have a very similar book as template (perhaps with the names of the main characters and a few locations changed), the de-novo assemblies are more hardcore in a sense as one would not know beforehand whether this would become a science book, a novel, a catalogue, or even several books. Also, every shre