help:

--version

show program's version number and exit

-h, --help

show this help message and exit

subcommands:

Clustering method

set

Cluster sequences within annotation sets.

all

Cluster all sequences regardless of annotation.

barcode

Cluster reads by clustering barcode sequences.

output files:

cluster-pass

clustered reads.

cluster-fail

raw reads failing clustering.

output annotation fields:

CLUSTER

a numeric cluster identifier defining the within-group cluster.