augur align¶
Align multiple sequences from FASTA.
usage: augur align [-h] --sequences SEQUENCES [--output OUTPUT]
[--nthreads NTHREADS] [--method {mafft}]
[--reference-name REFERENCE_NAME]
[--reference-sequence REFERENCE_SEQUENCE]
[--remove-reference] [--fill-gaps]
Named Arguments¶
- --sequences, -s
sequences in fasta or VCF format
- --output, -o
output file
- --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
strip insertions relative to reference sequence; 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