Better (but not perfect) HMW DNA extraction protocol

I wrote some time ago about the protocol I used to prepare HMW DNA for the new HA412 assembly. The advantage of that protocol is that it doesn’t need much tissue to start with, it’s quick and can work quite well. However, it is also quite unreliable, and will sometimes fail miserably.

To prepare HMW DNA for H. anomalus I tried a different protocol, suggested by Allen Van  Deynze at UC Davis. They used it on pepper to prepare HMW DNA for 10X linked reads (the same application I had in mind), and obtained fragments of average size ~150-200 Kb. The resulting 10X assembly was quite spectacular (N50 = 3.69 Mbp for a 3.21 Gbp genome) and was recently published. Continue reading