ARTIC V4.1 primer scheme for Omicron

[hoelzer]

We might need to add support for V4.1 soon:

https://twitter.com/Scalene/status/1466070415986544640

https://community.artic.network/t/sars-cov-2-v4-1-update-for-omicron-variant/342

[replikation]

we might want to implement also a "flexible" approach for a user to supply just a primer bed file?
otherwise, just copy V4 and add the primer bed to the dir :)
--primerV basically just specifies the primer dir to use which is located here: https://github.com/replikation/poreCov/tree/master/data/external_primer_schemes/nCoV-2019

therefore adding any dir and using the dir name in --primerV will work

[hoelzer]

k great!

we might want to implement also a "flexible" approach for a user to supply just a primer bed file?
actually, this might be helpful for a few users as well, yes. Only the primer bed is needed, right? Assuming then the primer positions are based on the correct reference Wuhan FASTA, which is right now always the case basically

[hoelzer]

We will test V4.1 soon, so would be good to get the primer BED in poreCov.

But yet can not find something here https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019

[hoelzer]

Spike-in Pools ARTIC 4.1.pptx

[MarieLataretu]

Not quite sure, what this comment means, but the arctic guys are also on it:
artic-network/artic-ncov2019#86 (comment)

In the mean time, I have here a scheme file for V4.1: nCoV-2019.scheme.bed.txt
Not sorted, just concatenated - not sure if this is important.

[hoelzer]

maybe that already does the trick, @MarieLataretu ! thx

Do you have time to add this as new primer kit to the pipeline? As @replikation wrote above, this should be relatively easy.

The best would be of course to use the "official" files once this issue artic-network/artic-ncov2019#86 (comment) is resolved. Maybe lets wait until tomorrow and see if the files are added then to the ARTIC primer repo :)

[MarieLataretu]

Sure, I can do a PR!

As I understand poreCov, only the scheme file is used, right?

Edit: I think seqrs needs also the primer sequences

[replikation]

just add a folder like this:
https://github.com/replikation/poreCov/tree/master/data/external_primer_schemes/nCoV-2019/VarSkipV1a

primer bed file and the fasta and fai file (can be copied). the dirname is the name for the --primerV flag.
seqrs is using the primer bed file
Make sure the filenames are the same (e.g. nCoV-2019.scheme.bed )

[hoelzer]

Thx @MarieLataretu ! once we have the structure already in, we can also easily update to the official files from the ARTIC network once they ar available