augur titers
Annotate a tree with actual and inferred titer measurements.
usage: augur titers [-h] {tree,sub} ...
Sub-commands
tree
tree model
augur titers tree [-h] --titers TITERS [TITERS ...] --tree TREE
[--allow-empty-model] [--attribute-prefix ATTRIBUTE_PREFIX]
--output OUTPUT
Named Arguments
- --titers
file with titer measurements
- --tree, -t
tree to perform fit titer model to
- --allow-empty-model
allow model to be empty
Default:
False
- --attribute-prefix
prefix for node attributes in the JSON output including cumulative titer drop (‘cTiter’) and per-branch titer drop (‘dTiter’). Set a prefix to disambiguate annotations from multiple tree model JSONs in the final Auspice JSON.
Default:
''
- --output, -o
JSON file to save titer model
sub
substitution model
augur titers sub [-h] --titers TITERS [TITERS ...] --alignment ALIGNMENT
[ALIGNMENT ...] --gene-names GENE_NAMES [GENE_NAMES ...]
[--tree TREE] [--allow-empty-model]
[--attribute-prefix ATTRIBUTE_PREFIX] --output OUTPUT
Named Arguments
- --titers
file with titer measurements
- --alignment
sequence to be used in the substitution model, supplied as fasta files
- --gene-names
names of the sequences in the alignment, same order assumed
- --tree, -t
optional tree to annotate fit titer model to
- --allow-empty-model
allow model to be empty
Default:
False
- --attribute-prefix
prefix for node attributes in the JSON output including cumulative titer drop (‘cTiterSub’) and per-substitution titer drop (‘dTiterSub’). Set a prefix to disambiguate annotations from multiple substitution model JSONs in the final Auspice JSON.
Default:
''
- --output, -o
JSON file to save titer model