FAQ: Is there any benefit to adding in a size selection (e.g., Circulomics® Short Read Eliminator) following extraction?

In NEB’s experience, a size selection step is usually not necessary upstream of ligation-based nanopore sequencing. When working with fresh, high-quality starting materials, the N50 read lengths are high (35 – 55 kb, depending on the sample) and an additional size selection of the HMW DNA will provide only marginal improvement in read length. However, when working with starting materials of lower quality, for example those which have been stored sub-optimally, or when working with samples that are very difficult to lyse (e.g., mouse tail) the resulting DNA will contain a larger portion of short fragments. In these cases, it may be useful to carry out an enrichment step for better sequencing results; any size selection product (e.g., Short Read Eliminator) can be used with the DNA isolated with the Monarch HMW DNA Extraction Kits.