augur align

Command-line arguments

Align multiple nucleotide sequences from FASTA. The “N” character is treated as missing or ambiguous sites, so aligning amino acid sequences is not supported.

usage: augur align [-h] [--config CONFIG] --sequences FASTA [FASTA ...]
                   [--output OUTPUT] [--nthreads NTHREADS] [--method {mafft}]
                   [--reference-name NAME] [--reference-sequence PATH]
                   [--remove-reference] [--fill-gaps]
                   [--existing-alignment FASTA] [--debug]

Named Arguments

--config

config file path

--sequences, -s

sequences to align

--output, -o

output file

Default: 'alignment.fasta'

--nthreads

number of threads to use; specifying the value ‘auto’ will cause the number of available CPU cores on your system, if determinable, to be used

Default: 1

--method

Possible choices: mafft

alignment program to use

Default: 'mafft'

--reference-name

strip insertions relative to reference sequence; use if the reference is already in the input sequences

--reference-sequence

Add this reference sequence to the dataset & strip insertions relative to this. Use if the reference is NOT already in the input sequences

--remove-reference

remove reference sequence from the alignment

Default: False

--fill-gaps

If gaps represent missing data rather than true indels, replace by N after aligning.

Default: False

--existing-alignment

An existing alignment to which the sequences will be added. The ouput alignment will be the same length as this existing alignment.

--debug

Produce extra files (e.g. pre- and post-aligner files) which can help with debugging poor alignments.

Default: False

Configuration

Options can also be specified in a YAML configuration file supplied to --config with the following top-level keys:

Option	Type	Description
sequences	file(s)	sequences to align
output	string	output file
nthreads	string	number of threads to use; specifying the value ‘auto’ will cause the number of available CPU cores on your system, if determinable, to be used
method	one of: mafft	alignment program to use
reference_name	string	strip insertions relative to reference sequence; use if the reference is already in the input sequences
reference_sequence	file	Add this reference sequence to the dataset & strip insertions relative to this. Use if the reference is NOT already in the input sequences
remove_reference	boolean	remove reference sequence from the alignment
fill_gaps	boolean	If gaps represent missing data rather than true indels, replace by N after aligning.
existing_alignment	file	An existing alignment to which the sequences will be added. The ouput alignment will be the same length as this existing alignment.
debug	boolean	Produce extra files (e.g. pre- and post-aligner files) which can help with debugging poor alignments.