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
UCHIME2 paper for details).
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.