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AUGUR(1) User Commands AUGUR(1)


augur - pipeline components for real-time virus analysis


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


Augur: A bioinformatics toolkit for phylogenetic analysis.


positional arguments:

Parse delimited fields from FASTA sequence names into a TSV and FASTA file.
Filter and subsample a sequence set.
Mask specified sites from a VCF 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

optional arguments:

show this help message and exit


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

March 2020 augur 6.4.2