Build STAG database for 16S amplicon

To build a database to classify amplicon data, you can use the same methods as for the genes. Where you have to consider that you need to select only the sequences that belong to the amplicon, and not the entire gene.

For example, if you want to design a classifier for the region V4 of the 16 rRNA gene, you will have to extract the V4 region from your database of training sequences. The taxonomy can stay the same. Additionally, you need to have a HMM file that is trained on the V4 region, which can be created from the extracted sequences (see also how to create a hmm file).