search

cov-lineages / pangolin

Software package for assigning SARS-CoV-2 genome sequences to global lineages.
GNU General Public License v3.0
428 stars 107 forks source link

How to use pangolin naming other vrius? #549

Open AceLi12138 opened 2 months ago

AceLi12138 commented 2 months ago

I want to use pangolin naming another vrius, but I don't know how to change the training dataset of pangolin how to re-train the model . I don't know if it is possible, but I think if users has the ability to name virus using pangolin, it will be great.

AngieHinrichs commented 2 months ago

Pangolin could be extended to support other viruses, but it would require some development work. The nextclade command line tool already has a mechanism to work with input datasets that (in theory) can be constructed for any virus. The nextclade team has added datasets for several viruses such as SARS-CoV-2, several influenza A subtypes, RSV and others. There are also some datasets contributed by the community. There is also a web version where you can see a list of viruses that are already supported and try it out.