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UCHIME2 algorithm
 
See also
 
uchime2_ref command
  uchime2_denovo command

UCHIME2 is an algorithm for detecting chimeric sequences. It is an update of the UCHIME algorithm with some new features. It is implemented in the uchime2_ref and uchime2_denovo commands. See UCHIME2 paper for details.

I do not recommend using uchime2_ref in a 16S or ITS analysis pipeline. The problem is that you will get high rates of both FPs and FNs unless you have denoised sequences, in which case the chimera removal is a special case which is built into the denoising code (see UCHIME2 paper for details).

It is better to use unoise or cluster_otus for chimera filtering. I believe that unoise is a better approach because it has better resolution: it reconstructs the biological sequences in the reads without 97% clustering. This enables you to resolve species and strains which are >97% similar to each other.

I recommend you use the largest available reference database for uchime2_ref, e.g. SILVA for 16S or UNITE for ITS. My previous advice to use a small, high-quality database was misguided (wrong!)-- you need a large database to get decent sensitivity, a small database like "gold" will probably be missing many parents in practice.