Multithreading is supported.
The -fastaout option specifies a FASTA output file for the unique sequences. Sequences are sorted by decreasing abundance.
The -fastqout option specifies a FASTQ output file for the unique sequences. Sequences are sorted by decreasing abundance.
The -tabbedout option specifies an output file in tabbed text format. The fields are: 1. input label, 2. output label (this is the input label of the first occurrence of the sequence, or the new label assigned to it if the -relabel option is used), 3. cluster number (zero-based, so 0 is the first unique sequence found, 1 is the second etc.), 4. member number in the cluster (zero -based), 5. input label of the first occurrence of the sequence (only if -relabel is specified).
The -uc output file is supported, but not other standard output files.
The -sizeout option specifies that size annotations should be added to the output sequence labels.
The -relabel option specifies a string that is used to re-label the dereplicated sequences. An integer is appended to the label.
E.g., -relabel Uniq will generate sequences labels Uniq1, Uniq2 ... etc. By default, the label of the first occurrence of the sequence is used.
The -minuniquesize option sets a minimum abundance. Unique sequences with a lower abundance are discarded. Default is 1, which means that all unique sequences are output.
The -topn N option specifies that only the first N sequences in order of decreasing abundance will be written to the output file.
Reverse-complemented matching for nucleotide sequences is supported by specifying -strand both.
usearch -fastx_uniques input.fasta -fastaout uniques.fasta -sizeout -relabel Uniq