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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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Improve Documentation #191

Closed oliverdrechsel closed 1 year ago

oliverdrechsel commented 2 years ago

Is your feature request related to a problem? Please describe. We're currently testing new Primer sets. As far as I can tell there is no documentation how to make porecov aware of new primer schemes that are not necessarily publicly available.

Describe the solution you'd like Add a chapter to the documentation.

Describe alternatives you've considered I've checked Readme to no avail.

Additional context none

hoelzer commented 2 years ago

Hi @oliverdrechsel yes, fully agree.

@replikation adding a short section about how to add primer sets via just cloning the repo and adding a new folder following a defined structure should be easy done?

And then, as we discussed in the issue about the V4.1 primer addition, it would be good to think about an even easier way that users can just provide their own Bed file following a defined structure.

oliverdrechsel commented 2 years ago

It would be also nice to know if the bed file needs to fit any specifics. We just recognised by trial and error (not sure, if all is true).

sorted by primer name, not position
primer naming needs to be primer_1_LEFT, primer_1_RIGHT. Further extensions of the name seem to be tolerated.

hoelzer commented 2 years ago

... and

it also seems that column5 should have the information about pool "1" or "2"
and something like:

*_56_LEFT_1
*_56_RIGHT_1alt

seems to fail when there is no

*_56_RIGHT_1

replikation commented 2 years ago

its mostly down to the artic assembly process as they are "parsing" and using the primer info/structure.
but i was thinking of allowing an optional "primer.bed" input file for which we could specify the necessary info/structure? (so people can easily add in house primer solutions)

hoelzer commented 2 years ago

Hi @replikation , yes exactly, an optional "primer.bed" input parameter would be great. We could then just describe in the README what the structure is that needs to be used, basically following the ARTIC scheme. This would make testing w/ new primer sets more easily. One could then still use the latest -r release and just provide some --custom-primer-bed foo.bed or so