The uchime_denovo command assumes amplicons as input, which must be annotated with abundances. This is because the de novo mode of the UCHIME algorithm relies on the assumption that a chimeric amplicon will be less abundant than its parents, because it will have undergone fewer rounds of amplification. See abundance skew for explanation.

Example using dereplication

usearch -derep_prefix reads.fasta -output amplicons.fasta -sizeoout
usearch -uchime_denovo amplicons.fasta -uchimeout results.uchime

Example using clustering

usearch -cluster_fast reads.fasta -id 0.99 -consout amplicons.fasta -sizeoout
usearch -uchime_denovo amplicons.fasta -uchimeout results.uchime