OTU / denoising pipeline
This example shows the minimum commands you need to get from overlapping paired reads to OTUs and denoised (ZOTU) sequences. In practice, you'll probably need to do more read preparation. There are 4,259 reads of a mock community which generate ~21 OTUs and ~22 ZOTUs. You need to set the environment variable $usearch to the name (or path) for your usearch binary file.
Download commands and data
Reads: right-click on ex_min2_reads.tar.gz and click Save As. Use tar -zxvf ex_min2_reads.tar.gz to extract.
Bash script: select all text below (ctrl+A) and copy/paste into a text editor, or right-click on ex_min2.bash and click Save As.