If your intent is to make a reference database based on clustered sequences, then yes you can use this approach. But if you are simply clustering your reads to generate OTUs for analyses, then you should use vsearch.
In general, we do not recommend clustering reads for the purposes of making a reference database as your ability to correctly assign taxonomy to your reads declines. This is covered in our RESCRIPt manuscript. Usually, clustering reference sequences is performed to reduce the file and memory size of the reference database when computational resources are limited.