--min_depth function - Githubissues

replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data

https://case-group.github.io/

GNU General Public License v3.0

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--min_depth function #158

Closed omarkr8 closed 2 years ago

omarkr8 commented 2 years ago

what does the min_depth option do exactly? I imagine it is independent of the min_coverage related to RKI? I also do not see min_depth being referenced when starting the pipeline (unlike other parameters you can adjust).

replikation commented 2 years ago

its the minimum read depth for the artic assembly. the default is a depth of 20x.
Every nucleotide below that will be masked to "N"
ill add that to the references
it was kind of useful if you have a bad sequencing run you can reduce the depth to at least find out what lineage it might be
however the accuracy is not really good with so few reads to polish errors then.

replikation commented 2 years ago

it is also described in the --help

--min_depth nucleotides below min depth will be masked to "N" [default 20]

omarkr8 commented 2 years ago

Thanks, I did manage to find it in documentation. Just wasnt sure how the min_depth was being used. So for bad runs, reducing the min_depth helps with reducing Ns at the cost of confidence in the consensus.

replikation commented 2 years ago

yes. I also clarified some help messages (available in the next release)