See also
OTU / denoising pipeline
Read preparation
Sometimes machine-specific sequences appear in the reads. For example, 454 reads often start with the control sequence TCAG which is used for calibrarion, though the four letters may come in a different order, and they may have been stripped before you get the reads. If the sequence has a fixed length and appears at the start of the read, it can be stripped by the fastx_truncate command using the same strategy used to strip primer sequences. If you're not sure exactly what is in your reads, machine-specific sequences are often noticable when you align OTUs to a reference database.