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mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs
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How does Flye resolve 'unbridged' repeats? #677

Closed Matteo-Paini closed 7 months ago

Matteo-Paini commented 7 months ago

Hi, thanks for you work on this tool and for the continuous upgrades! I used Flye for several genome assemblies and it always worked perfectly.

I just have a thoeretical question: I studied the paper of Flye and I'm trying to understand how it resolves the "unbridged repeats". Can someone explain this passage to me?

Thanks in advanced!

mikolmogorov commented 7 months ago

Hi,

In short, Flye doesn't :) We used to have a trestle module, but it is now deprecated.

Misha

Matteo-Paini commented 7 months ago

Hello Misha, thanks for your reply!

So, does the depreciation of the Trestle module affect the accuracy of the final assembly?

A way to avoid this “unresolved bridges” could be the usage of ultralong reads by ont?

mikolmogorov commented 7 months ago

It may affect slightly, but Trestle was inactive for a few years now. The longer the reads, the more repeats can potentially be resolved.