Augur command documentation

You’ll find automatically generated documentation of all augur commands below. A few commands have many options or are a common source of difficulty and we provide separate pages explaining their usage and most important arguments using examples. Such pages are currently available for

The automatically generated documentation of all subcommands follows.

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]
           [--tree-builder-args TREE_BUILDER_ARGS]

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)

--tree-builder-args

extra arguments to be passed directly to the executable of the requested tree method (e.g., –tree-builder-args=”-czb”)

Default: “”

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]
             [--keep-polytomies] [--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

--keep-polytomies

Do not attempt to resolve polytomies

Default: False

--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: “GENE SITE ALT DISPLAY_NAME FEATURE”. For nucleotide sites, GENE can be “nuc” (or column excluded entirely for all-nuc sites). “DISPLAY_NAME” can be blank or excluded entirely.

--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 ...] [--no-normalization]

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

--no-normalization

disable normalization of LBI by the maximum value

Default: False

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:

  1. root: the root and all nodes in the tree (the previous default for all distances)

  2. ancestor: each tip from a current season and its immediate ancestor (optionally, from a previous season)

  3. 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]
                  [--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]
                  [--minimal-clade-size MINIMAL_CLADE_SIZE]
                  [--minimal-clade-size-to-estimate MINIMAL_CLADE_SIZE_TO_ESTIMATE]
                  [--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

--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

--minimal-clade-size

minimal number of tips a clade must have for its diffusion frequencies to be reported

Default: 0

--minimal-clade-size-to-estimate
minimal number of tips a clade must have for its diffusion frequencies to be estimated

by the diffusion likelihood; all smaller clades will inherit frequencies from their parents

Default: 10

--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] [--output-tree OUTPUT_TREE]
             [--output-sequence OUTPUT_SEQUENCE] [--output-meta OUTPUT_META]
             [--minify-json] [--new-schema] [--output-main OUTPUT_MAIN]
             [--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 ...]]
             {v1} ...

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

--output-tree

JSON file name that is passed on to auspice (e.g., zika_tree.json).

--output-sequence

JSON file name that is passed on to auspice (e.g., zika_seq.json).

--output-meta

JSON file name that is passed on to auspice (e.g., zika_meta.json).

--minify-json

export JSONs without indentation or line returns

Default: False

--new-schema

export JSONs using new v2 schema (in development)

Default: False

--output-main

Main JSON file name that is passed on to auspice (e.g., zika.json).

--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’]

Sub-commands:

v1

Mimic augur v6’s way of calling augur export. Contains a subset of the arguments available to augur export.

augur export v1 [-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]
                [--output-tree OUTPUT_TREE]
                [--output-sequence OUTPUT_SEQUENCE]
                [--output-meta OUTPUT_META] [--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

--output-tree

JSON file name that is passed on to auspice (e.g., zika_tree.json).

--output-sequence

JSON file name that is passed on to auspice (e.g., zika_seq.json).

--output-meta

JSON file name that is passed on to auspice (e.g., zika_meta.json).

--minify-json

export JSONs without indentation or line returns

Default: False

validate

Validate a set of JSON files intended for visualization in auspice.

augur validate [-h] --json JSON [JSON ...] [--new-schema]

Named Arguments

--json

JSONs to validate

--new-schema

use nexflu JSON schema

Default: False

version

Print the version of augur.

augur version [-h]