To handle multi-step clustering, USEARCH provides a mechanism to propagate cluster size annotations. If the ‑sizein option is specified, input sequences are required to have a size annotation. If the ‑sizeout option is specified, size annotations are added to the output labels. If both -sizein and -sizeout are given, then the output size for a cluster takes into account the input sizes.
Typical use is:
1. First clustering or dereplication step in the pipeline uses -sizeout.
2. Subsequent clustering steps use both -sizein and -sizeout.
If another program is used before the first USEARCH step, then it is up to you to write scripts to produce size annotations for USEARCH.