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