Sequence Assembly - De-novo Vs. Mapping Assembly

De-novo Vs. Mapping Assembly

In sequence assembly, two different types can be distinguished:

1. de-novo: assembling short reads to create full-length (sometimes novel) sequences (see de novo transcriptome assembly)
2. mapping: assembling reads against an existing backbone sequence, building a sequence that is similar but not necessarily identical to the backbone sequence

In terms of complexity and time requirements, de-novo assemblies are orders of magnitude slower and more memory intensive than mapping assemblies. This is mostly due to the fact that the assembly algorithm needs to compare every read with every other read (an operation that has a complexity of O(n2) but can be reduced to O(n log(n)). 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, or a novel, or a catalogue etc.