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Various seasonal-cov improvements #43

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@genehack genehack commented Dec 18, 2024 •
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Description of proposed changes

  • Locks clock rate for 229E and OC43
  • Various best practices updates:
    • use "raw" string quoting
    • use abbreviated authors as "authors", full author as "full authors"
    • use recommended TSV handling best practices
  • Add frequencies panel
  • Excludes some HKU1 and NL63 strains to improve tree rooting

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@genehack
Lock clock rates for 229E and OC43 [#36]
968c4d9
@genehack
Use abbreviated authors as "authors"; full authors as "full authors"
9b5d38f
@genehack
Add tip frequencies, enable frequencies panel [#41]
a86fb3c
@genehack
Tweak color-by -- re-order, add author
c291cdd
@genehack
Missing backquote
122a209
@genehack
Drop HKU1 strains from Chow et al
17faa78 
With these strains included, the HKU1 tree roots badly — these fall in
between the two effective clades in the tree, causing the root to not
be properly positioned in between them.
@genehack
Exclude lower quality HKU1 sequences
cb5eb36 
This is all sequences (as of ~15 Dec 2024) with >6k Ns or <80%
coverage. This was determined by exporting the Nextstrain tree over to
Nextclade, dropping the entire Nextstrain sequences.fasta on the
Nextclade tree, then filtering/sorting samples by both N count and
coverage percentage.
@genehack
Drop a couple NL63 sequences
22619be 
As suggested by Trevor.
@genehack
Update TSV handling per best practices [#42]
a60dae7 
Verified that metadata file outputs are unchanged by this revision.
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@joverlee521 joverlee521 Awaiting requested review from joverlee521

@kistlerk kistlerk Awaiting requested review from kistlerk

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