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rpetit3 / dragonflye

:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads
GNU General Public License v3.0
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Coverage of "0"? #24

Closed MalbertRogers closed 8 months ago

MalbertRogers commented 11 months ago

What does a coverage of 0 (for a config) in the "flye-info.txt" mean? I don't think these contigs end up in the final assembly file anyway, but I am curious as to how and why it is being reported as such, since it obviously doesn't make much sense.

rpetit3 commented 10 months ago

I apologize for the very late response to this.

I tried to dig this out of the Flye repo (https://github.com/fenderglass/Flye), and could not come to a conclusion on what it means to have 0 coverage.

I wonder if it is worth asking over on the Flye repo?

incoherentian commented 10 months ago

Flye is probably only using the best match when calculating read coverage post-contig-generation. Odd that Flye generated those artifact contigs to start with, but them not being in the final assembly just shows that Flye / dragonflye is doing its job well :)

rpetit3 commented 8 months ago

Hi @MalbertRogers

I'm going to go ahead and close this, please feel free to reopen