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Edinburgh-Genome-Foundry / DnaWeaver

A route planner for DNA assembly
https://dnaweaver.genomefoundry.org
MIT License
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What role cut_spread_radius plays in circular sequence decomposition? #6

Open andrewshvv opened 3 years ago

andrewshvv commented 3 years ago

I am debugging why the circular sequence decomposition does not work for me, and it seems cut_spread_radius kinda plays a role in it. The documentation is lacking information about it.

Could you please share a bit of information about it?

Zulko commented 3 years ago

Sorry for the lack of documentation. See slides 221-225 here. When you use the coarse-grain/fine-grain decomposition approach, there is a first quick sequence decomposition to find good cuts, then a refinement around these cuts, to find even better cuts. The cut_spread_radius is how many nucleotides away the better cuts can be from the good cuts.

I'm not 100% sure how this could impact circular sequence decomposition (but I understand that it could), it may depend on how you define the circularity. It's difficult to say without a minimal failing example.