Recent advancements in optical mapping and DNA sequencing have thus allowed for the construction of improved genome assemblies with greater contiguity. Optical mapping in particular enables greater genome comparison and aids the identification o large-scale structural variations, which is an important goal to accomplish for the advantages and insight it gives in the fields of animal breeding and medical research. Optical mapping is also used in microbiology, strain typing, and epidemiological studies.
Advances in DNA sequencing have improved genomic research by producing more complete genome assemblies and detecting larger SV. It is still, however, often not yet sufficient to produce data of desired reference-grade quality. Optical mapping is one of a few methods used to help overcome the shortcomings in sequencing data, to produce a chromosome-level genome assembly for species with large and complex genomes.
Optical mapping is an important complimentary method and, though it cannot in any way replace DNA sequencing for its lack of nucleotide information, it provides vital structural information that DNA sequencing cannot. Thus, one of the greatest advantages of optical mapping is that it can map long molecular lengths at low cost. Its shortcoming lies in resolution.
The low resolution of optical mapping can partially be helped by applying certain enzymes or with the use of DNA labelling. These methods, however, have been applied and made for humans and it is uncertain if transference is possible. When transferred, it tends to churn out faulty information (false negatives, positives, etc.) and so this method is largely untrustworthy when applied on any other species than human beings.
In any case, optical mapping has come far and serves a vital role in genomic research, creating, along with DNA sequencing, improved genome assemblies of high quality and accuracy.
Sources: Computational and Structural Biotechnology Journal; Advances in optical mapping for genomic research (Yuxuan Yuan, Claire Yik-Lok Chung, Ting-Fung Chang)