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| AUGUR(1) |
User Commands |
AUGUR(1) |
NAME¶
augur - pipeline components for real-time virus analysis
SYNOPSIS¶
augur [-h] {parse, filter, mask, align, tree, refine, ancestral,
translate, reconstruct-sequences, clades, traits, sequence-traits, lbi,
distance, titers, frequencies, export, validate, version, import} ...
DESCRIPTION¶
Augur: A bioinformatics toolkit for phylogenetic analysis.
OPTIONS¶
positional arguments:¶
- 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 files related to augur consumption or export.
- version
- Print the version of augur.
- import
- Import analyses into augur pipeline from other systems
optional arguments:¶
- -h, --help
- show this help message and exit
AUTHOR¶
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.
