NAME¶

SYNOPSIS¶

Trim 3´-end adaptor contaminants off sequence files. If no output file is specified, scythe will use stdout.

OPTIONS¶

 -p, --prior prior (default: 0.300)
 -q, --quality-type quality type, either illumina, solexa, or sanger (default: sanger)
 -m, --matches-file matches file (default: no output)
 -o, --output-file output trimmed sequences file (default: stdout)
 -t, --tag add a tag to the header indicating Scythe cut a sequence (default: off)
 -n, --min-match smallest contaminant to consider (default: 5)
 -M, --min-keep filter sequences less than or equal to this length (default: 35)
      --quiet don´t output statistics about trimming to stdout (default: off)
      --help display this help and exit
      --version output version information and exit


These are the quality encoding schemes scythe recognises (see ´--quality´)
  phred     PHRED quality scores (e.g. from Roche 454). ASCII with no
            offset, range: [4, 60].
  sanger    Sanger are PHRED ASCII qualities with an offset of 33,
            range: [0, 93]. From NCBI SRA, or Illumina pipeline 1.8+.
  solexa    Solexa (also very early Illumina -- pipeline < 1.3).
            ASCII offset of 64, range: [-5, 62]. Uses a different
            quality-to-probabilities conversion than other schemes.
  illumina  Illumina output from pipeline versions between 1.3 and 1.7.
            ASCII offset of 64, range: [0, 62]

FILES¶

adaptors.fasta: Provide contaminant sequences as a fasta-formatted file.
                 See ´/usr/share/doc/scythe/illumina_adaptors.fa´.
                 N.B.: Index/Barcode sequences should be substituted for Ns in
                 the example adaptor file.

AUTHOR¶