The goal of this PR is to create a tree using a 450bp region of the N gene ("N450") that is highly represented on NCBI for measles. Addresses github issue https://github.com/nextstrain/measles/issues/13
General steps include:
Add a reference sequence that is 450bp of the N gene from the reference that is used for the whole-genome tree
Align all sequences against the N450 reference using Nextclade
Filter by alignment length
Subsample by date and geography
Use Snakemake wildcards to generate and export phylogeny
Many of these changes follow those made for E gene trees in the dengue repo
Description of proposed changes
The goal of this PR is to create a tree using a 450bp region of the N gene ("N450") that is highly represented on NCBI for measles. Addresses github issue https://github.com/nextstrain/measles/issues/13
General steps include:
Many of these changes follow those made for E gene trees in the dengue repo
Related issue(s)
13
Checklist