Home Software Services About Contact     
 
USEARCH v11

sortbysize command

 
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.

Example

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