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
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
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.
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.
© 2015-2019 Trevor Bedford and Richard Neher