Updated H3N2 reference to A/Perth/16/2009.

seattleflu / augur-build

the (in development) augur build for understanding influenza dynamics in Seattle

https://seattleflu.org

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Updated H3N2 reference to A/Perth/16/2009. #13

Closed cassiawag closed 5 years ago

cassiawag commented 5 years ago

This commit should address #9 & #10. I swapped out all reference genomes for H3N2 for A/Perth/16/2009 segments, and I also updated the script create_ref_genome.py to add header information for reference_{lineage}_genome.gb.

trvrb commented 5 years ago

@cassiawag: Thank you! Can you rebase these onto two separate PRs? Best practice is to have PRs be issue-specific.

cassiawag commented 5 years ago

Done! This PR now only updates the reference sequences in the config folder; should fix #10 @trvrb

cassiawag commented 5 years ago

In Snakefile, just updated def reference_strain(wildcards): to specify A/Perth/16/2009 for H3N2.

trvrb commented 5 years ago

@cassiawag: Thanks for putting in this PR. I now believe that A/Beijing/32/1992 is working well as a reference strain. I realize now moving to A/Perth/16/2009 will require updating

https://github.com/seattleflu/augur-build/blob/master/config/clades_h3n2_ha.tsv
https://github.com/seattleflu/augur-build/blob/master/config/exclude-sites_h3n2_genome.txt
https://github.com/seattleflu/augur-build/blob/master/config/ha_masks.tsv Better to wait on this. I'm going to close this PR, but let's keep the ref_genome branch around.