SSUplex extracts small-subunit rRNA (16S/18S) sequences from environmental sequencing reads and sorts them by origin so each set can be routed to the appropriate downstream classifier. It is a Rust reimplementation of the Metaxa2 SSU extraction and origin-classification step, using nhmmer to scan both strands. HMM profiles are not bundled; build them from the Metaxa2 SSU profile database as described in the README.