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sortbysize command
Commands > FASTA/Q files, Reads, Miscellaneous
See also
Abundance sort
  UCLUST sort order
  Global trimming

Sort sequences by decreasing size annotation, which usually refers to the size of a cluster. The size is specified by a field size=N; in the sequence label, where N is an integer. The ‑minsize and -maxsize options can be used to specify a minimum and maximum size, respectively.

Output is written to a FASTA file using the -fastaout option and/or a FASTQ file using the -fastqout option.

For most applications, it is recommended that sequences are globally trimmed before clustering and abundance sorting.

The -relabel prefix option can be used to generate sequential labels for the sorted sequences. The output label is prefixN where N=1, 2, 3 etc. If -sizeout is used, a size annotation will be appended to the sequential label.

The -topn N option specifies that no more than N sequences should be output.


usearch -sortbysize seqs.fasta -fastaout seqs_sorted.fasta -minsize 4