Commands > OTU analysis, Chimeras
Chimera detection using an improved version of the
UCHIME2 algorithm. This command is designed
for chimera detection in a set of denoised amplicons. The input sequences must have
size=nnn; annotations giving amplicon
abundances. See UCHIME2 paper for details.
The main change from the original UCHIME2 algorithm is that the default
minimum abundance skew (abskew option) is now 16 rather than 2. Based on
recent results (not yet written up), I believe that with abskew=2 there are
many more false positive chimera detections. Perfect chimera detection is
not possible due to unbiquitous fake models (see UCHIME2 paper), but with
abskew=16 I believe there is a much more reasonable balance between false
positives and false negatives.
Note that the unoise command does chimera
filtering automatically using exactly the same algorithm as uchime3_denovo, so
there is typically no reason to use this command in a USEARCH-based
pipeline. It is mainly useful for chimera filtering of amplicons that were
denoised by third-party software. In particular, I believe that the DADA2
(at least through v1.4.0) has a high false positive rate for chimera
detection, and it would therefore be better to filter chimeras using
uchime3_denovo rather than the native DADA2 code.
The input uchime3_denovo command
be denoised amplicons. It is not
designed to handle noisy reads as input (even if they have been quality
filtered), or to take OTUs as input.
The following output files are supported:
(tabbed text filename)
-nonchimeras (FASTA file with
-chimeras (FASTA file with chimeric
-alnout (text file with human-readable alignments)
Chimera detection in an OTU
I do not recommend using uchime2_ref
or uchime3_denovo in an OTU clustering pipeline. The
cluster_otus command has built-in de
filtering which works very well for most data. Using uchime2_ref as a
post-processing step is quite likely to discard some false positives that
are actually good sequences.
usearch -uchime2_denovo denoised.fa -uchimeout out.txt
-chimeras ch.fa -nonchimeras