Hi @dereneaton@isaacovercast, is there a method of obtaining consensus sequences for all loci? I'd like to blast these against a chloroplast and mitochondrial genome and remove those loci that match from the downstream assembly if possible. Cheers
@Ollie_W_White_twitter Deren reminded me of a nice trick you can use to filter out chloroplast/mitochondrial reads. If you concatenate the chloroplast and mitochondrial reference genomes together you can use the denovo-reference assembly method to filter out all reads that map to these.