Hi all, wondering if anyone has some thoughts on the best way to get (full-length?) barcode genes out of Illumina shotgun data?

Maybe cmsearch against an Rfam model of interest? That works with 16S but it depends on which genes you are looking into

Yeah, I’ve been wondering about an approach like that (though probably with HMMs rather than CMs), but I’m concerned it would be slow, and might require multiple models for different clades. I’m mainly looking to pull out COI and rbcl barcodes.