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AUGUR(1) User Commands AUGUR(1)

NAME

augur - pipeline components for real-time virus analysis

DESCRIPTION

usage: augur [-h]

{parse, index, filter, mask, align, tree, refine, ancestral, translate, reconstruct-sequences, clades, traits, sequence-traits, lbi, distance, titers, frequencies, export, validate, version, import, measurements} ...

Augur: A bioinformatics toolkit for phylogenetic analysis.

positional arguments:

{parse, index, filter, mask, align, tree, refine, ancestral, translate, reconstruct-sequences, clades, traits, sequence-traits, lbi, distance, titers, frequencies, export, validate, version, import, measurements}
Parse delimited fields from FASTA sequence names into a TSV and FASTA file.
Count occurrence of bases in a set of sequences.
Filter and subsample a sequence set.
Mask specified sites from a VCF or FASTA file.
Align multiple sequences from FASTA.
Build a tree using a variety of methods.
Refine an initial tree using sequence metadata.
Infer ancestral sequences based on a tree.
Translate gene regions from nucleotides to amino acids.
Reconstruct alignments from mutations inferred on the tree
Assign clades to nodes in a tree based on amino-acid or nucleotide signatures.
Infer ancestral traits based on a tree.
Annotate sequences based on amino-acid or nucleotide signatures.
Calculate LBI for a given tree and one or more sets of parameters.
Calculate the distance between sequences across entire genes or at a predefined subset of sites.
Annotate a tree with actual and inferred titer measurements.
infer frequencies of mutations or clades
Export JSON files suitable for visualization with auspice.
Validate files related to augur consumption or export.
Print the version of augur.
Import analyses into augur pipeline from other systems
Create JSON files suitable for visualization within the measurements panel of Auspice.

options:

show this help message and exit

AUTHOR


This manpage was written by Étienne Mollier for the Debian distribution and can be used for any other usage of the program.

June 2022 augur 16.0.1