uchime2_denovo command
Chimera detection using the UCHIME2 algorithm. This command is designed for chimera detection in denoised amplicons. The input sequences must have size=nnn; annotations giving amplicon abundances. See UCHIME2 paper for details.
Not that the unoise command does chimera filtering automatically (using UCHIME2 denoised de novo mode), 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 are denoised by third-party software. For example, the DADA2 removeBimeraDenovo() function misses some chimeras that are found by uchime2_denovo (tested version of DADA2 was 0.99.10).
The uchime2_denovo command is not designed to taker noisy reads as input (even if they have been quality filtetered) or to take OTUs as input.
The following output files are supported:
-uchimeout out.txt (tabbed text)
-nonchimeras non.fa (FASTA file with non-chimeric sequences)
-chimeras ch.fa (FASTA file with chimeric sequences)
-alnout aln.txt (alignments)
Chimera detection in an OTU
pipeline
I do not recommend using uchime2_ref
or uchime2_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 -uchime2_denovo denoised.fa -uchimeout out.txt
-chimeras ch.fa -nonchimeras
nonch.fa