sort is one of the core subprograms of SeqFu, that allows sorting FASTA sequences by length, printing only unique sequences (unless --keep-duplicates is used).

Usage: sort [options] [<inputfile> ...]

 Sort FASTA sequences by length, printing only unique sequences.

 All input files are pooled: duplicates are removed across files and
 a single sorted output is printed. When a sequence occurs more than once,
 the name of its first occurrence is kept. Sequences of equal length are
 printed in input order.

 FASTQ is not supported: FASTQ input is accepted, but quality scores are
 discarded and the output is always FASTA.

Options:
  -p, --prefix STRING    Rename sequences as STRING1, STRING2, ...
  -s, --strip-comments   Remove sequence comments
  -k, --keep-duplicates  Keep identical sequences as separate records
  --asc                  Ascending order
  -v, --verbose          Verbose output
  -h, --help             Show this help

Notes

• FASTQ is not supported. Sorting is designed for FASTA files. FASTQ files are read, but quality scores are dropped and the output is FASTA (a warning is printed to the standard error).
• Multiple files are pooled into a single sorted output. Without --keep-duplicates, a sequence present in more than one file is printed once.
• Duplicates: identical sequences (case-sensitive comparison) are collapsed into the first occurrence, keeping its name and comment. Use --keep-duplicates to print every record.
• Ties: sequences with the same length are printed in the order they appear in the input, so the output is reproducible.
• The whole input is loaded in memory before sorting.

Example

seqfu sort --asc -p seq_ contigs.fa > sorted.fa

Screenshot