Augur commands

Augur commands — for instance augur parse or augur align — are designed to be stand alone commands performing one bioinformatics task.

All augur commands are run via the augur program — you can see a list of these by running augur --help. More details for each command can be seen via augur <command> --help (e.g. augur traits --help).

For an online list of augur commands & their arguments please see the augur documentation [external link].


As of augur version 5.1.1, these are the available commands (generated via augur --help):

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

All source code is freely available under the terms of the GNU Affero General Public License. Screenshots etc may be used as long as a link to nextstrain.org is provided.

This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions. Special thanks to Kristian Andersen, Allison Black, David Blazes, Peter Bogner, Matt Cotten, Ana Crisan, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Becky Garten, Dylan George, Ian Goodfellow, Nathan Grubaugh, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Sebastian Maurer-Stroh, Louise Moncla, Oliver Pybus, Andrew Rambaut, Colin Russell, Pardis Sabeti, Katherine Siddle, Kristof Theys, Dave Wentworth, Shirlee Wohl and Nathan Yozwiak for comments, suggestions and data sharing.

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© 2015-2019 Trevor Bedford and Richard Neher