To check if the genome of your species of interest is suitable for Optical Genome Mapping on the Bioanao Saphyr, you should check the distribution of labeling sequence motifs. For this purpose, Bionano provides in silico digestion tools with the “Label Density Calculator” program. “Bionano Access” also has such a feature. Both programs are available from this webpage: https://bionanogenomics.com/support/software-downloads/
The preferred label density for nickases is 8 to 15 labels per 100kb. For the methylase-based DLE-1 protocol, the label density can be even higher.
Nt.BspQI and Nb.BssSI are the preferred nickases. They work pretty consistently.
Provided the label densities are sufficient the preferred labeling method would be DLE-1, followed by both Nt.BspQI or Nb.BssSI.
Other nickases should only be used in emergencies.
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