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