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wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
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Filter based on minimum horizontal coverage #195

Open ntromas opened 8 months ago

ntromas commented 8 months ago

Hi!

Is there a way to filter output based on minimum horizontal coverage? To validate that the reads covered most of the genome (instead of one part if the MAGs is potentially a chimera...)

Cheers,

Nico

wwood commented 8 months ago

Hi,

Do you mean covered_fraction? Or something else? I'm not sure what horizontal coverage is sorry. ben

ntromas commented 8 months ago

Hi Ben,

Sorry for the confusion. I mean breadth. I guess the output option "covered_bases" might help. I initially thought that breadth was the parameter --min-covered-fraction.

Nico

Le sam. 13 janv. 2024 06 h 50, Ben J Woodcroft @.***> a écrit :

Hi,

Do you mean covered_fraction? Or something else? I'm not sure what horizontal coverage is sorry. ben

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