Dereplicates sequences using prefix matching.
Multithreading is supported.
The ‑fastaout option is used to specify a FASTA file to contain the unique sequences. Sequences are sorted by decreasing cluster size.
The ‑fastqout option is used to specify a FASTQ file to contain the unique sequences. Sequences are sorted by decreasing cluster size.
The ‑uc output file is supported, but not other standard output files.
The ‑sizeout option may be used to specify that size annotations are added to the unique sequence labels. See cluster sizes.
The ‑minuniquesize option may be used to set a minimum size for a cluster; unique sequences with smaller clusters are not included in the output file.
The -minseqlength option may be used to specify a minimum sequence length. Using this option may significantly improve execution speed if there are very short sequences in the input which are not needed in the output.
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 D_ will generate sequences labels D_1, D_2 ... etc.
The -topn N option specifies that only the largest N clusters will be written to the output file.
usearch -derep_prefix input.fasta -fastaout uniques.fasta -sizeout -minseqlength 64