Question: different extractions for Hybrid assembly
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gravatar for mariachiaracascarano
6 months ago by
mariachiaracascarano10 wrote:

HI everybody! I recently sequenced a bacterial genome using Nextera XT library and I would now like to improve my assembly with long reads from MinION.

The starting DNA extraction has been frozen and thaw a couple of times and I am afraid that the quality of my DNA is not gonna be optimal to obtain long reads.

Considering the extraction is been made from a pure isolate preserved in cryobeads (-80) I was thinking to make a new fresh extraction from the same beads and run MinION on the fresh extraction.

My question now is, is this likely to create problems during the hybrid assembly? Is it essential to run them from same extractions? I will probably follow a pipeline Canu + Pilon or spades hybrid...

Thanks for any kind of suggestions, Chiara

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