8.4 years ago by
I've used optical maps in order to look at assembled 454 contigs and it has worked brilliantly. You can see how much of your genome is covered by your assembly and where (and how big) the gaps are.
Opgen data is simple and you can get 2 outputs. One is hierarchical tree based on the similarity between whatever number of genomes you send in (and any others in their database I think). This gives you a quick indication of the similarity between genomes. The second output is the optical map which is simply a rectangular box split up by vertical lines wherever the restriction enzyme occurs in the sequence.
Once you have your contigs, Opgen software will in silico digest them and place them onto the optical map where the patterns match. Sometimes your contigs will be too small for this and this is an issue with sequencing and the assembly process. From my own experience with a 4.5Mb genome, it is a good tool to use as opposed to mate pair genome sequencing for orientating contigs and getting a idea of how much sequence you are missing etc.