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
Parse delimited fields from FASTA sequence names into a TSV and FASTA file.
index
Count occurrence of bases in a set of sequences.
filter
Filter and subsample a sequence set.
mask
Mask specified sites from a VCF or FASTA 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
measurements
Create JSON files suitable for visualization within the measurements panel of Auspice.

options:

-h, --help
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.