Typical USEARCH commands for OTU clustering

These commands were used for OTU accuracy benchmark testing.

Step		Command line
Quality filtering and global trimming		-fastq_filter reads.fastq -fastaout reads.fasta -fasta_truncqual 15 -fasta_trunclen 250
Dereplication		-derep_fulllength reads.fasta -output derep.fasta -sizeout
Pre-clustering		-cluster_smallmem derep.fasta -centroids pre.fasta -sizeout -id 0.99 -maxdiffs 1
Discard singletons		-sortbysize pre.fasta -output pre2.fasta -minsize 2
OTU clustering		-cluster_otus pre2.fasta -otus otus.fasta