search

nextstrain / nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
https://clades.nextstrain.org
MIT License
204 stars 58 forks source link

ENH: Primers should not have to match reference 100%, use mismatch-tolerant alignment #953

Open corneliusroemer opened 1 year ago

corneliusroemer commented 1 year ago

Matthijs Welkers mentioned that he had tried to use Nextclade's primer feature with monkeypox (he has published an amplicon tiling scheme for nanopore) but that he got an error when he tried using his primers because some of them were mutated with respect to the reference used by Nextclade.

It would be possible and very useful if primers would align in an error tolerant way with any reference - so that one can upload any primers, not just primers that are subsets of the reference sequence.

This is technically doable, would be a natural extension of the current work on improving seed-matching.

ammaraziz commented 4 months ago

If I may jump in here, if you're looking at expanding the primer checking features of nextclade, it would be super awesome to have the primer checking step as a separate command within nextclade cli so that I can run nextclade primer-check without having to perform.