seqfu derep

derep is one of the core subprograms of SeqFu, that allows the dereplication of FASTA and FASTQ files.

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

Options:
  -k, --keep-name              Do not rename sequence, but use the first sequence name
  -i, --ignore-size            Do not count 'size=INT;' annotations (they will be stripped in any case)
  -m, --min-size=MIN_SIZE      Print clusters with size equal or bigger than INT sequences [default: 0]
  -p, --prefix=PREFIX          Sequence name prefix [default: seq]
  -5, --md5                    Use MD5 as sequence name (overrides other parameters)
  -j, --json=JSON_FILE         Save dereplication metadata to JSON file
  -s, --separator=SEPARATOR    Sequence name separator [default: .]
  -w, --line-width=LINE_WIDTH  FASTA line width (0: unlimited) [default: 0]
  -l, --min-length=MIN_LENGTH  Discard sequences shorter than MIN_LEN [default: 0]
  -x, --max-length=MAX_LENGTH  Discard sequences longer than MAX_LEN [default: 0]
  -c, --size-as-comment        Print cluster size as comment, not in sequence name
  --add-len                    Add length to sequence
  -v, --verbose                Print verbose messages
  -h, --help                   Show this help

Size values

By default the program will add the number of identical sequences found to the sequence name, as USEARCH does:

>seq.1;size=18335
CTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTACAGTATTCTTTTTGCCAGCGCTTAATTGCGCGGCGAAAAAACCTTACACACAGTGTTTTTTGTTATTACAAGAACTTTTGCTTTGGTCTGGACTAGAAATAGTTTGGGCCAGAGGTTTACTGAACTAAACTTCAATATTTATATTGAATTGTTATTTATTTAATTGTCAATTTGTTGATTAAATTCAAAAAATCTTCAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC
>seq.2;size=4085
CTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTGAAGTTTAACTCAGAGGGTTGTAGCTGGCTCCTCCAAGAGCATGTGCACGCCCTTTGTCTTTACTCTTTTCCACCTGTGCACCTTTTGTAGACCATGAGTGAACTCTCGAGAGCGTTGGCAACGACGTGATCGGTTTGGGGATTTGCGTTCAGCTTTCCCTGTAGCTCGTGGTTTATGTCTTATAAACTCTATAGTCTGTTTTGAATGTCTTATGGGTTTTGCGCTGTAATGGTGCGACCTTTATAAACTATACAACTTTTAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC
>seq.3;size=2453
CTTGGTCATTTAGAGGAAGTAAGAGAGAAATGTATAAACTCATAATTGACGAATGATAATTGTTATTGAAGTTTTTGTAAAGGGGCTTCTTTATGAATAAGGGATACACGTTTGACGATATGATTAATACCATGATGCCCCTGGCCCTTTGACGGCTCGGCAAAGGGTGAAGGAATTTACTGCACGGTCAGGCCCTCGTCGCATCGATGAAGAACGCAGC

To keep the size separate from the sequence name it's possible to used -c (--size-as-comment):

>seq.1 size=18335
CTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTACAGTATTCTTTTTGCCAGCGCTTAATTGCGCGGCGAAAAAACCTTACACACAGTGTTTTTTGTTATTACAAGAACTTTTGCTTTGGTCTGGACTAGAAATAGTTTGGGCCAGAGGTTTACTGAACTAAACTTCAATATTTATATTGAATTGTTATTTATTTAATTGTCAATTTGTTGATTAAATTCAAAAAATCTTCAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC
>seq.2 size=4085
CTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTGAAGTTTAACTCAGAGGGTTGTAGCTGGCTCCTCCAAGAGCATGTGCACGCCCTTTGTCTTTACTCTTTTCCACCTGTGCACCTTTTGTAGACCATGAGTGAACTCTCGAGAGCGTTGGCAACGACGTGATCGGTTTGGGGATTTGCGTTCAGCTTTCCCTGTAGCTCGTGGTTTATGTCTTATAAACTCTATAGTCTGTTTTGAATGTCTTATGGGTTTTGCGCTGTAATGGTGCGACCTTTATAAACTATACAACTTTTAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC
>seq.3 size=2453
CTTGGTCATTTAGAGGAAGTAAGAGAGAAATGTATAAACTCATAATTGACGAATGATAATTGTTATTGAAGTTTTTGTAAAGGGGCTTCTTTATGAATAAGGGATACACGTTTGACGATATGATTAATACCATGATGCCCCTGGCCCTTTGACGGCTCGGCAAAGGGTGAAGGAATTTACTGCACGGTCAGGCCCTCGTCGCATCGATGAAGAACGCAGC

Summing dereplicated outputs

If the input files were already dereplicated printing the "size" of the cluster, derep will sum the size values.

Screenshot