uchime3_denovo command
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 to uchime3_denovo
must
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:
-uchimeout (tabbed text filename)
-nonchimeras (FASTA file with non-chimeric sequences)
-chimeras (FASTA file with chimeric sequences)
-alnout (text file with human-readable alignments)
Chimera detection in an OTU pipeline
I do
not recommend
using uchime2_ref or uchime3_denovo in an OTU clustering pipeline. The
cluster_otus command
has built-in de novo chimera 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.
Example
usearch -uchime3_denovo denoised.fa -uchimeout out.txt -chimeras ch.fa -nonchimeras nonch.fa
