Is it possible to prevent translation when using genemap?

I would like to extract the individual genes from a genomic dataset but when I use genemap it automatically translates to peptides. Is there a way to keep this in nucleotide format?

The commands I’m using are below:

–input-fasta data/DENV1_NC/dengue_denv1.fasta
–output-tsv output/nextclade.tsv
–input-dataset data/DENV1_NC
–output-tree output/nextclade.auspice.json
–output-dir output/
–output-basename nextclade

Hi @Rhys1234,

Sorry for the late reply.

Nextclade does not write genes in nucleotide format, so currently you would need to extract them yourself, based on alignment (--output-fasta) and genemap.

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