I am working on shotgun genomic sequences on plants, and I wanted to mapp my sequences into a list of genes of references (eg. BUSCO) in order to retrieve a consensus for each of my own sample and to compare them after in phylogenetic analyses.
I ran DIAMOND with my reads/contigs (from SPAdes) into my proteins of reference and I identified different hits. But i am wondering how I can retrieve my consensus (in nucleotide) for each gene of reference, and if there is a correct way to proceed as in samtools with mpileup function. Have you any idea?
Thanks, Best regards