augur translate¶
Translate gene regions from nucleotides to amino acids.
usage: augur translate [-h] [--tree TREE]
[--ancestral-sequences ANCESTRAL_SEQUENCES]
--reference-sequence REFERENCE_SEQUENCE
[--genes GENES [GENES ...]]
[--output-node-data OUTPUT_NODE_DATA]
[--alignment-output ALIGNMENT_OUTPUT]
[--vcf-reference-output VCF_REFERENCE_OUTPUT]
[--vcf-reference VCF_REFERENCE]
Named Arguments¶
- --tree
prebuilt Newick – no tree will be built if provided
- --ancestral-sequences
JSON (fasta input) or VCF (VCF input) containing ancestral and tip sequences
- --reference-sequence
GenBank or GFF file containing the annotation
- --genes
genes to translate (list or file containing list)
- --output-node-data
name of JSON file to save aa-mutations to
- --alignment-output
write out translated gene alignments. If a VCF-input, a .vcf or .vcf.gz will be output here (depending on file ending). If fasta-input, specify the file name like so: ‘my_alignment_%GENE.fasta’, where ‘%GENE’ will be replaced by the name of the gene
- --vcf-reference-output
fasta file where reference sequence translations for VCF input will be written
- --vcf-reference
fasta file of the sequence the VCF was mapped to