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Yellow Fever Virus Nextclade Dataset Tree

This workflow creates a phylogenetic tree that can be used as part of a Nextclade dataset to assign clades to yellow fever virus samples based on Mutebi et al. (J Virol. 2001 Aug;75(15):6999-7008) and Bryant et al. (PLoS Pathog. 2007 May 18;3(5):e75).

  • Build a tree using samples from the ingest output, with the following sampling criteria:
    • Force-include the following samples:
      • genotype reference strains from the 2 papers cited above
  • Assign genotypes to each sample and internal nodes of the tree with augur clades, using clade-defining mutations in defaults/clades.tsv
  • Provide the following coloring options on the tree:
    • Genotype assignment from augur clades

The clades we annotate (Clade I-VII) are roughly equivalent with the following genotypes as described in the aforementioned two papers:

Clade Genotype
Clade I Angola
Clade II East Africa
Clade III East Central/Africa
Clade IV West Africa I
Clade V West Africa II
Clade VI South America I
Clade VII South America II

(N.b., this table is available as a TSV in this repo, at nextclade/defaults/clade-to-genotype.tsv.)

How to create a new tree

  • Run the workflow: nextstrain build .
  • Inspect the output tree by comparing genotype assignments from the following sources:
    • augur clades output
  • If unwanted samples are present in the tree, add them to defaults/dropped_strains.tsv and re-run the workflow
  • If any changes are needed to the clade-defining mutations, add changes to defaults/clades.tsv and re-run the workflow
  • Repeat as needed