USEARCH manual > algorithms > OTU clustering
OTU commands
 
Following are typical commands for OTU clustering from preprocessed reads. This reproduces the example command lines from OTU clustering in a convenient form for copy and pasting into your editor.

usearch --derep_fulllength reads.fa -sizeout   -output derep.fa

usearch -cluster_smallmem derep.fa -id 0.99  -centroids denoised.fa -sizein -sizeout

-sortbysize denoised.fa -output denoised.fas   -minsize 3

usearch -uchime_denovo denoised.fas -nonchimeras nonch_denovo.fasta

usearch -uchime_ref nonch_denovo.fasta -db gold_refdb.fasta -strand both \
  -nonchimeras nonch_ref.fasta

usearch -sortbysize nonch_ref.fasta -output sorted.fasta

usearch -cluster_smallmem sorted.fasta -id 0.97 -sizein -sizeout -centroids otus.fasta

usearch -sortbysize otus.fasta -minsize 4 -output otus_minsiz4.fasta