Augur command¶
All of Augur’s commands are accessed through the augur
program.
For example, to infer ancestral sequences from a tree, you’d run augur ancestral
.
Each command is documented below.
You can also run each command with the --help
option, for example augur tree --help
, for more information at the command-line.
usage: augur [-h]
{parse,filter,mask,align,tree,refine,ancestral,translate,reconstruct-sequences,clades,traits,sequence-traits,lbi,distance,titers,frequencies,export,validate,version}
...
Sub-commands:¶
parse¶
Parse delimited fields from FASTA sequence names into a TSV and FASTA file.
augur parse [-h] --sequences SEQUENCES [--output-sequences OUTPUT_SEQUENCES]
[--output-metadata OUTPUT_METADATA] [--fields FIELDS [FIELDS ...]]
[--separator SEPARATOR] [--fix-dates {dayfirst,monthfirst}]
Named Arguments¶
- --sequences, -s
sequences in fasta or VCF format
- --output-sequences
output sequences file
- --output-metadata
output metadata file
- --fields
fields in fasta header
- --separator
separator of fasta header
Default: “|”
- --fix-dates
Possible choices: dayfirst, monthfirst
attempt to parse non-standard dates and output them in standard YYYY-MM-DD format
filter¶
Filter and subsample a sequence set.
augur filter [-h] --sequences SEQUENCES --metadata METADATA
[--min-date MIN_DATE] [--max-date MAX_DATE]
[--min-length MIN_LENGTH] [--non-nucleotide] [--exclude EXCLUDE]
[--include INCLUDE] [--priority PRIORITY]
[--sequences-per-group SEQUENCES_PER_GROUP]
[--group-by GROUP_BY [GROUP_BY ...]]
[--exclude-where EXCLUDE_WHERE [EXCLUDE_WHERE ...]]
[--include-where INCLUDE_WHERE [INCLUDE_WHERE ...]] --output
OUTPUT
Named Arguments¶
- --sequences, -s
sequences in fasta or VCF format
- --metadata
metadata associated with sequences
- --min-date
minimal cutoff for numerical date
- --max-date
maximal cutoff for numerical date
- --min-length
minimal length of the sequences
- --non-nucleotide
exclude sequences that contain illegal characters
Default: False
- --exclude
file with list of strains that are to be excluded
- --include
file with list of strains that are to be included regardless of priorities or subsampling
- --priority
file with list priority scores for sequences (strain priority)
- --sequences-per-group
subsample to no more than this number of sequences per category
- --group-by
categories with respect to subsample; two virtual fields, “month” and “year”, are supported if they don’t already exist as real fields but a “date” field does exist
- --exclude-where
Exclude samples matching these conditions. Ex: “host=rat” or “host!=rat”. Multiple values are processed as OR (matching any of those specified will be excluded), not AND
- --include-where
Include samples with these values. ex: host=rat. Multiple values are processed as OR (having any of those specified will be included), not AND. This rule is applied last and ensures any sequences matching these rules will be included.
- --output, -o
output file
mask¶
Mask specified sites from a VCF file.
augur mask [-h] --sequences SEQUENCES --mask MASK [--output OUTPUT]
Named Arguments¶
- --sequences, -s
sequences in VCF format
- --mask
locations to be masked in BED file format
- --output, -o
output file
align¶
Align multiple sequences from FASTA.
augur align [-h] --sequences SEQUENCES [--output OUTPUT] [--nthreads NTHREADS]
[--method {mafft}] [--reference-name REFERENCE_NAME]
[--reference-sequence REFERENCE_SEQUENCE] [--remove-reference]
[--fill-gaps]
Named Arguments¶
- --sequences, -s
sequences in fasta or VCF format
- --output, -o
output file
- --nthreads
number of threads to use; specifying the value ‘auto’ will cause the number of available CPU cores on your system, if determinable, to be used
Default: 1
- --method
Possible choices: mafft
alignment program to use
Default: “mafft”
- --reference-name
strip insertions relative to reference sequence; use if the reference is already in the input sequences
- --reference-sequence
strip insertions relative to reference sequence; use if the reference is NOT already in the input sequences
- --remove-reference
remove reference sequence from the alignment
Default: False
- --fill-gaps
if gaps represent missing data rather than true indels, replace by N after aligning
Default: False
tree¶
Build a tree using a variety of methods.
augur tree [-h] --alignment ALIGNMENT [--method {fasttree,raxml,iqtree}]
[--output OUTPUT]
[--substitution-model {HKY,GTR,HKY+G,GTR+G,GTR+R10}]
[--nthreads NTHREADS] [--vcf-reference VCF_REFERENCE]
[--exclude-sites EXCLUDE_SITES]
Named Arguments¶
- --alignment, -a
alignment in fasta or VCF format
- --method
Possible choices: fasttree, raxml, iqtree
tree builder to use
Default: “iqtree”
- --output, -o
file name to write tree to
- --substitution-model
Possible choices: HKY, GTR, HKY+G, GTR+G, GTR+R10
substitution model to use. Specify ‘none’ to run ModelTest. Currently, only available for IQTREE.
Default: “GTR”
- --nthreads
number of threads to use; specifying the value ‘auto’ will cause the number of available CPU cores on your system, if determinable, to be used
Default: 1
- --vcf-reference
fasta file of the sequence the VCF was mapped to
- --exclude-sites
file name of one-based sites to exclude for raw tree building (BED format in .bed files, DRM format in tab-delimited files, or one position per line)
refine¶
Refine an initial tree using sequence metadata.
augur refine [-h] [--alignment ALIGNMENT] --tree TREE [--metadata METADATA]
[--output-tree OUTPUT_TREE] [--output-node-data OUTPUT_NODE_DATA]
[--timetree] [--coalescent COALESCENT] [--clock-rate CLOCK_RATE]
[--clock-std-dev CLOCK_STD_DEV] [--root ROOT [ROOT ...]]
[--keep-root] [--covariance] [--no-covariance]
[--date-format DATE_FORMAT] [--date-confidence]
[--date-inference {joint,marginal}]
[--branch-length-inference {auto,joint,marginal,input}]
[--clock-filter-iqd CLOCK_FILTER_IQD]
[--vcf-reference VCF_REFERENCE]
[--year-bounds YEAR_BOUNDS [YEAR_BOUNDS ...]]
Named Arguments¶
- --alignment, -a
alignment in fasta or VCF format
- --tree, -t
prebuilt Newick
- --metadata
tsv/csv table with meta data for sequences
- --output-tree
file name to write tree to
- --output-node-data
file name to write branch lengths as node data
- --timetree
produce timetree using treetime
Default: False
- --coalescent
coalescent time scale in units of inverse clock rate (float), optimize as scalar (‘opt’), or skyline (‘skyline’)
- --clock-rate
fixed clock rate
- --clock-std-dev
standard deviation of the fixed clock_rate estimate
- --root
rooting mechanism (‘best’, least-squares’, ‘min_dev’, ‘oldest’) OR node to root by OR two nodes indicating a monophyletic group to root by. Run treetime -h for definitions of rooting methods.
Default: “best”
- --keep-root
do not reroot the tree; use it as-is. Overrides anything specified by –root.
Default: False
- --covariance
Account for covariation when estimating rates and/or rerooting. Use –no-covariance to turn off.
Default: True
- --no-covariance
Default: True
- --date-format
date format
Default: “%Y-%m-%d”
- --date-confidence
calculate confidence intervals for node dates
Default: False
- --date-inference
Possible choices: joint, marginal
assign internal nodes to their marginally most likely dates, not jointly most likely
Default: “joint”
- --branch-length-inference
Possible choices: auto, joint, marginal, input
branch length mode of treetime to use
Default: “auto”
- --clock-filter-iqd
clock-filter: remove tips that deviate more than n_iqd interquartile ranges from the root-to-tip vs time regression
- --vcf-reference
fasta file of the sequence the VCF was mapped to
- --year-bounds
specify min or max & min prediction bounds for samples with XX in year
ancestral¶
Infer ancestral sequences based on a tree.
augur ancestral [-h] --tree TREE [--alignment ALIGNMENT] [--output OUTPUT]
[--output-node-data OUTPUT_NODE_DATA]
[--output-sequences OUTPUT_SEQUENCES]
[--inference {joint,marginal}] [--vcf-reference VCF_REFERENCE]
[--output-vcf OUTPUT_VCF] [--keep-ambiguous]
[--keep-overhangs]
Named Arguments¶
- --tree, -t
prebuilt Newick
- --alignment, -a
alignment in fasta or VCF format
- --output, -o
name of JSON file to save mutations and ancestral sequences to
- --output-node-data
name of JSON file to save mutations and ancestral sequences to
- --output-sequences
name of FASTA file to save ancestral sequences to (FASTA alignments only)
- --inference
Possible choices: joint, marginal
calculate joint or marginal maximum likelihood ancestral sequence states
Default: “joint”
- --vcf-reference
fasta file of the sequence the VCF was mapped to
- --output-vcf
name of output VCF file which will include ancestral seqs
- --keep-ambiguous
do not infer nucleotides at ambiguous (N) sites on tip sequences (leave as N). Always true for VCF input.
Default: False
- --keep-overhangs
do not infer nucleotides for gaps (-) on either side of the alignment
Default: False
translate¶
Translate gene regions from nucleotides to amino acids.
augur translate [-h] [--tree TREE] [--ancestral-sequences ANCESTRAL_SEQUENCES]
--reference-sequence REFERENCE_SEQUENCE
[--genes GENES [GENES ...]] [--output OUTPUT]
[--alignment-output ALIGNMENT_OUTPUT]
[--vcf-reference-output VCF_REFERENCE_OUTPUT]
[--vcf-reference VCF_REFERENCE]
Named Arguments¶
- --tree
prebuilt Newick – no tree will be built if provided
- --ancestral-sequences
JSON (fasta input) or VCF (VCF input) containing ancestral and tip sequences
- --reference-sequence
GenBank or GFF file containing the annotation
- --genes
genes to translate (list or file containing list)
- --output
name of JSON files for aa mutations
- --alignment-output
write out translated gene alignments. If a VCF-input, a .vcf or .vcf.gz will be output here (depending on file ending). If fasta-input, specify the file name like so: ‘my_alignment_%GENE.fasta’, where ‘%GENE’ will be replaced by the name of the gene
- --vcf-reference-output
fasta file where reference sequence translations for VCF input will be written
- --vcf-reference
fasta file of the sequence the VCF was mapped to
reconstruct-sequences¶
Reconstruct alignments from mutations inferred on the tree
augur reconstruct-sequences [-h] --tree TREE [--gene GENE] --mutations
MUTATIONS [--vcf-aa-reference VCF_AA_REFERENCE]
[--internal-nodes] [--output OUTPUT]
Named Arguments¶
- --tree
tree as Newick file
- --gene
gene to translate (list or file containing list)
- --mutations
json file containing mutations mapped to each branch and the sequence of the root.
- --vcf-aa-reference
fasta file of the reference gene translations for VCF format
- --internal-nodes
include sequences of internal nodes in output
Default: False
- --output
clades¶
Assign clades to nodes in a tree based on amino-acid or nucleotide signatures.
augur clades [-h] [--tree TREE] [--mutations MUTATIONS [MUTATIONS ...]]
[--reference REFERENCE [REFERENCE ...]] [--clades CLADES]
[--output OUTPUT]
Named Arguments¶
- --tree
prebuilt Newick – no tree will be built if provided
- --mutations
JSON(s) containing ancestral and tip nucleotide and/or amino-acid mutations
- --reference
fasta files containing reference and tip nucleotide and/or amino-acid sequences
- --clades
TSV file containing clade definitions by amino-acid
- --output
name of JSON files for clades
traits¶
Infer ancestral traits based on a tree.
augur traits [-h] --tree TREE --metadata METADATA --columns COLUMNS
[COLUMNS ...] [--confidence]
[--sampling-bias-correction SAMPLING_BIAS_CORRECTION]
[--output OUTPUT]
Named Arguments¶
- --tree, -t
tree to perform trait reconstruction on
- --metadata
tsv/csv table with meta data
- --columns
metadata fields to perform discrete reconstruction on
- --confidence
record the distribution of subleading mugration states
Default: False
- --sampling-bias-correction
a rough estimate of how many more events would have been observed if sequences represented an even sample. This should be roughly the (1-sum_i p_i^2)/(1-sum_i t_i^2), where p_i are the equilibrium frequencies and t_i are apparent ones.(or rather the time spent in a particular state on the tree)
- --output, -o
Default: “traits.json”
sequence-traits¶
Annotate sequences based on amino-acid or nucleotide signatures.
augur sequence-traits [-h] [--ancestral-sequences ANCESTRAL_SEQUENCES]
[--translations TRANSLATIONS]
[--vcf-reference VCF_REFERENCE]
[--vcf-translate-reference VCF_TRANSLATE_REFERENCE]
[--features FEATURES] [--count {traits,mutations}]
[--label LABEL] [--output OUTPUT]
Named Arguments¶
- --ancestral-sequences
nucleotide alignment to search for sequence traits in
- --translations
AA alignment to search for sequence traits in (can include ancestral sequences)
- --vcf-reference
fasta file of the sequence the nucleotide VCF was mapped to
- --vcf-translate-reference
fasta file of the sequence the translated VCF was mapped to
- --features
file that specifies sites defining the features in a tab-delimited format “GENOMIC_POSITION ALT_BASE DRUG AA(optional)”
- --count
Possible choices: traits, mutations
Whether to count traits (ex: # drugs resistant to) or mutations
Default: “traits”
- --label
How to label the counts (ex: Drug_Resistance)
Default: “# Traits”
- --output, -o
output json with sequence features
lbi¶
Calculate LBI for a given tree and one or more sets of parameters.
augur lbi [-h] --tree TREE --branch-lengths BRANCH_LENGTHS --output OUTPUT
--attribute-names ATTRIBUTE_NAMES [ATTRIBUTE_NAMES ...] --tau TAU
[TAU ...] --window WINDOW [WINDOW ...]
Named Arguments¶
- --tree
Newick tree
- --branch-lengths
JSON with branch lengths and internal node dates estimated by TreeTime
- --output
JSON file with calculated distances stored by node name and attribute name
- --attribute-names
names to store distances associated with the corresponding masks
- --tau
tau value(s) defining the neighborhood of each clade
- --window
time window(s) to calculate LBI across
distance¶
Calculate the distance between sequences across entire genes or at a predefined subset of sites.
Distance calculations require selection of a comparison method (to determine which sequences to compare) and a distance map (to determine the weight of a mismatch between any two sequences).
Comparison methods¶
Comparison methods include:
root: the root and all nodes in the tree (the previous default for all distances)
ancestor: each tip from a current season and its immediate ancestor (optionally, from a previous season)
pairwise: all tips pairwise (optionally, all tips from a current season against all tips in previous seasons)
Ancestor and pairwise comparisons can be calculated with or without information about the current season. When no dates are provided, the ancestor comparison calculates the distance between each tip and its immediate ancestor in the given tree. Similarly, the pairwise comparison calculates the distance between all pairs of tips in the tree.
When the user provides a “latest date”, all tips sampled after that date belong to the current season and all tips sampled on that date or prior belong to previous seasons. When this information is available, the ancestor comparison calculates the distance between each tip in the current season and its last ancestor from a previous season. The pairwise comparison only calculates the distances between tips in the current season and those from previous seasons.
When the user also provides an “earliest date”, pairwise comparisons exclude tips sampled from previous seasons prior to the given date. These two date parameters allow users to specify a fixed time interval for pairwise calculations, limiting the computationally complexity of the comparisons.
Distance maps¶
Distance maps are defined in JSON format with two required top-level keys. The default key specifies the numeric value (integer or float) to assign to all mismatches by default. The map key specifies a dictionary of weights to use for distance calculations. These weights are indexed hierarchically by gene name and one-based gene coordinate and are assigned in either a sequence-independent or sequence-dependent manner. The simplest possible distance map calculates Hamming distance between sequences without any site-specific weights, as shown below:
{
"name": "Hamming distance",
"default": 1,
"map": {}
}
Sequence-independent distances are defined by gene and position using a numeric value of the same type as the default value (integer or float). The following example is a distance map for antigenic amino acid substitutions near influenza A/H3N2 HA’s receptor binding sites. This map calculates the Hamming distance between amino acid sequences only at seven positions in the HA1 gene:
{
"name": "Koel epitope sites",
"default": 0,
"map": {
"HA1": {
"145": 1,
"155": 1,
"156": 1,
"158": 1,
"159": 1,
"189": 1,
"193": 1
}
}
}
Sequence-dependent distances are defined by gene, position, and sequence pairs where the from sequence in each pair is interpreted as the ancestral state and the to sequence as the derived state. The following example is a distance map that assigns asymmetric weights to specific amino acid substitutions at a specific position in the influenza gene HA1:
{
"default": 0.0,
"map": {
"HA1": {
"112": [
{
"from": "V",
"to": "I",
"weight": 1.192
},
{
"from": "I",
"to": "V",
"weight": 0.002
}
]
}
}
}
The distance command produces a JSON output file in standard “node data” format that can be passed to augur export. In addition to the standard nodes field, the JSON includes a params field that describes the mapping of attribute names to requested comparisons and distance maps and any date parameters specified by the user. The following example JSON shows a sample output when the distance command is run with multiple comparisons and distance maps:
{
"params": {
"attributes": ["ep", "ne", "ne_star", "ep_pairwise"],
"compare_to": ["root", "root", "ancestor", "pairwise"],
"map_name": [
"wolf_epitope",
"wolf_nonepitope",
"wolf_nonepitope",
"wolf_epitope"
],
"latest_date": "2009-10-01"
},
"nodes": {
"A/Afghanistan/AF1171/2008": {
"ep": 7,
"ne": 6,
"ne_star": 1,
"ep_pairwise": {
"A/Aichi/78/2007": 1,
"A/Argentina/3509/2006": 2
}
}
}
}
augur distance [-h] --tree TREE --alignment ALIGNMENT [ALIGNMENT ...]
--gene-names GENE_NAMES [GENE_NAMES ...] --attribute-name
ATTRIBUTE_NAME [ATTRIBUTE_NAME ...] --compare-to
{root,ancestor,pairwise} [{root,ancestor,pairwise} ...] --map
MAP [MAP ...] [--date-annotations DATE_ANNOTATIONS]
[--earliest-date EARLIEST_DATE] [--latest-date LATEST_DATE]
--output OUTPUT
Named Arguments¶
- --tree
Newick tree
- --alignment
sequence(s) to be used, supplied as FASTA files
- --gene-names
names of the sequences in the alignment, same order assumed
- --attribute-name
name to store distances associated with the given distance map; multiple attribute names are linked to corresponding positional comparison method and distance map arguments
- --compare-to
Possible choices: root, ancestor, pairwise
type of comparison between samples in the given tree including comparison of all nodes to the root (root), all tips to their last ancestor from a previous season (ancestor), or all tips from the current season to all tips in previous seasons (pairwise)
- --map
JSON providing the distance map between sites and, optionally, sequences present at those sites; the distance map JSON minimally requires a ‘default’ field defining a default numeric distance and a ‘map’ field defining a dictionary of genes and one-based coordinates
- --date-annotations
JSON of branch lengths and date annotations from augur refine for samples in the given tree; required for comparisons to earliest or latest date
- --earliest-date
earliest date at which samples are considered to be from previous seasons (e.g., 2019-01-01). This date is only used in pairwise comparisons. If omitted, all samples prior to the latest date will be considered.
- --latest-date
latest date at which samples are considered to be from previous seasons (e.g., 2019-01-01); samples from any date after this are considered part of the current season
- --output
JSON file with calculated distances stored by node name and attribute name
titers¶
Annotate a tree with actual and inferred titer measurements.
augur titers [-h] {tree,sub} ...
Sub-commands:¶
tree¶
tree model
augur titers tree [-h] --titers TITERS [TITERS ...] --tree TREE
[--allow-empty-model] --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
- --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] --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
- --output, -o
JSON file to save titer model
frequencies¶
infer frequencies of mutations or clades
augur frequencies [-h] --method {diffusion,kde} --metadata METADATA
[--regions REGIONS [REGIONS ...]]
[--pivot-interval PIVOT_INTERVAL] [--min-date MIN_DATE]
[--max-date MAX_DATE] [--tree TREE]
[--include-internal-nodes]
[--minimal-clade-size MINIMAL_CLADE_SIZE]
[--alignments ALIGNMENTS [ALIGNMENTS ...]]
[--gene-names GENE_NAMES [GENE_NAMES ...]]
[--ignore-char IGNORE_CHAR]
[--minimal-frequency MINIMAL_FREQUENCY]
[--narrow-bandwidth NARROW_BANDWIDTH]
[--wide-bandwidth WIDE_BANDWIDTH]
[--proportion-wide PROPORTION_WIDE] [--weights WEIGHTS]
[--weights-attribute WEIGHTS_ATTRIBUTE] [--censored]
[--stiffness STIFFNESS] [--inertia INERTIA]
[--output-format {auspice,nextflu}] [--output OUTPUT]
Named Arguments¶
- --method
Possible choices: diffusion, kde
method by which frequencies should be estimated
- --metadata
tab-delimited metadata including dates for given samples
- --regions
region to subsample to
Default: [‘global’]
- --pivot-interval
number of months between pivots
Default: 3
- --min-date
minimal pivot value
- --max-date
maximal pivot value
- --tree, -t
tree to estimate clade frequencies for
- --include-internal-nodes
calculate frequencies for internal nodes as well as tips
Default: False
- --minimal-clade-size
minimal size of a clade to have frequencies estimated
Default: 0
- --alignments
alignments to estimate mutations frequencies for
- --gene-names
names of the sequences in the alignment, same order assumed
- --ignore-char
character to be ignored in frequency calculations
Default: “”
- --minimal-frequency
minimal all-time frequencies for a trajectory to be estimates
Default: 0.05
- --narrow-bandwidth
the bandwidth for the narrow KDE
Default: 0.08333333333333333
- --wide-bandwidth
the bandwidth for the wide KDE
Default: 0.25
- --proportion-wide
the proportion of the wide bandwidth to use in the KDE mixture model
Default: 0.2
- --weights
a dictionary of key/value mappings in JSON format used to weight KDE tip frequencies
- --weights-attribute
name of the attribute on each tip whose values map to the given weights dictionary
- --censored
calculate censored frequencies at each pivot
Default: False
- --stiffness
parameter penalizing curvature of the frequency trajectory
Default: 10.0
- --inertia
determines how frequencies continue in absense of data (inertia=0 -> go flat, inertia=1.0 -> continue current trend)
Default: 0.0
- --output-format
Possible choices: auspice, nextflu
format to export frequencies JSON depending on the viewing interface
Default: “auspice”
- --output, -o
JSON file to save estimated frequencies to
export¶
Export JSON files suitable for visualization with auspice.
augur export [-h] --tree TREE --metadata METADATA [--reference REFERENCE]
[--reference-translations REFERENCE_TRANSLATIONS] --node-data
NODE_DATA [NODE_DATA ...] [--auspice-config AUSPICE_CONFIG]
[--colors COLORS] [--lat-longs LAT_LONGS] [--new-schema]
[--output-main OUTPUT_MAIN] [--output-tree OUTPUT_TREE]
[--output-sequence OUTPUT_SEQUENCE] [--output-meta OUTPUT_META]
[--title TITLE] [--maintainers MAINTAINERS [MAINTAINERS ...]]
[--maintainer-urls MAINTAINER_URLS [MAINTAINER_URLS ...]]
[--geography-traits GEOGRAPHY_TRAITS [GEOGRAPHY_TRAITS ...]]
[--extra-traits EXTRA_TRAITS [EXTRA_TRAITS ...]]
[--panels PANELS [PANELS ...]] [--minify-json]
Named Arguments¶
- --tree, -t
tree to perform trait reconstruction on
- --metadata
tsv file with sequence meta data
- --reference
reference sequence for export to browser, only vcf
- --reference-translations
reference translations for export to browser, only vcf
- --node-data
JSON files with meta data for each node
- --auspice-config
file with auspice configuration
- --colors
file with color definitions
- --lat-longs
file latitudes and longitudes, overrides built in mappings
- --new-schema
export JSONs using nexflu schema
Default: False
- --output-main
Main JSON file name that is passed on to auspice (e.g., zika.json).
- --output-tree
JSON file name that is passed on to auspice (e.g., zika_tree.json). Only used with –nextflu-schema
- --output-sequence
JSON file name that is passed on to auspice (e.g., zika_seq.json). Only used with –nextflu-schema
- --output-meta
JSON file name that is passed on to auspice (e.g., zika_meta.json). Only used with –nextflu-schema
- --title
Title to be displayed by auspice
Default: “Analysis”
- --maintainers
Analysis maintained by
Default: [‘’]
- --maintainer-urls
URL of maintainers
Default: [‘’]
- --geography-traits
What location traits are used to plot on map
- --extra-traits
Metadata columns not run through ‘traits’ to be added to tree
- --panels
What panels to display in auspice. Options are : xxx
Default: [‘tree’, ‘map’, ‘entropy’]
- --minify-json
export JSONs without indentation or line returns
Default: False