The depoly command collapses all homopolymers in a FASTA or FASTQ input file into single letters. A homopolymer is a run of two or more consecutive identical letters, e.g. AA or TTT. So the sequence AGGTTTC would be collapsed to AGTC. This can be useful with 454 reads, which tend to have errors in the lengths of homopolymers.
The output file is always in FASTA format, and is specified using the -fastaout option.
Example
usearch -depoly reads.fa -fastaout reads_collapsed.fa