Adding H5N1 primer and reference files

[ajlail98]

Hi there! David O'Connor's lab has had some success sequencing off of this tiled amplicon approach, so we'd love to share with the community.
I have tried to use primal-page, but with these files I get something failing in the primerbed validation step. Could you help me get the file to whatever it's supposed to be? I figured a PR with the files themselves would give you enough information to work with, and then we can merge the fixed files. Let me know how I can help figure this out or if I need to add more files!

[ChrisgKent]

Hi,

Thanks for committing some schemes to labs!

Creating the files with primal-page create is the best way of adding schemes, however I see that primal-page's error messages are not very clear. I'll fix that.

The breaking issues are;

• Some of the primernames (col 4) are invalid (HPAIPB1_7-2_LEFT and HPAIPB1_7-2_RIGHT)!
• The primernames are in the form {name}_{amplicon-number}_{LEFT|RIGHT} we like to enforce {name}_{amplicon-number}_{LEFT|RIGHT}_{primer-number} as it makes the schemes much more repairable with spike in primers. This can be fixed by addending _1 to each primername

Some other questions \ issues.

• The pool column (col 6) has values of 0,3,20,40,254. Primal-page will accept these, but I don't think they are the genuine pools the primers go into.
• The reference genomes are RNA.
• The file containing the genome ie primerschemes/h5n1 should match the scheme name in info.json. This should be fixed when breaking changes are modified and primal-page create is used

[ChrisgKent]

avrl-h5n1-hpai.zip

I've attached an example of the fixed version of the files!