README_clustering_OTUs

The 4_clustering_swarm_with_chim_filter_pbs.sh/4_clustering_swarm_with_chim_filter_slurm.sh scripts run as a pbs and slurm job, respectively.
The script does not have arguments (options), it is positional:

./4_clustering_swarm_with_chim_filter_pbs.sh <prefix> <dereplicated fastas directory> <threads>
./4_clustering_swarm_with_chim_filter_slurm.sh <prefix> <dereplicated fastas directory> <threads>

The first part does the global dereplication from the dereplicated by samples step. 
The second part is the clustering itself, please take a look in SWARM arguments and documentation: https://github.com/torognes/swarm. 
The third part is the sorting by size.
The forth part is the chimera search.
The last part edits the abundance annotation from ';size=X;' to '_X'

Several outputs are generated:
global_dereplication.sh >> prefix_global_derep.fas
clustering_swarm >>  prefix_cluster.struct
			               prefix_cluster.stats
		                 prefix_cluster_representatives.fas
			               prefix_cluster.swarms
chimera_checking >> prefix_cluster_representatives.uchime

all those outputs will be necessary to build the OTU table.