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uchime_denovo command

The uchime_denovo command is deprecated for use in OTU clustering pipelines because cluster_otus is more effective.

Performs de novo chimera detection using the UCHIME algorithm.

I generally recommend pooling samples from all PCR runs rather than running samples individually.

See UCHIME score for parameters.

The input file must contain estimated amplicons with abundances specified by size annotations.

Multithreading is not supported.

See uchime output files for output options.

The ‑abskew option sets the abundance skew, which defaults to 2.0.


usearch -uchime_denovo amplicons.fasta -uchimeout results.uchime