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UCHIME2 algorithm

See also
uchime2_ref command
  uchime3_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 command. See UCHIME2 paper for details.

The uchmie2_denovo command is obsolete. It is replaced by the uchime3_denovo command which implements the chimera filtering step in unoise3. This the same algorithm described in the UCHIME2 paper, except that parameters have been adjusted to reduce the number of false positives.

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 unoise3 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.