NAME

       scythe - Bayesian adaptor trimmer

SYNOPSIS

       scythe -t sanger -a /path/to/adaptors.fasta [options] <sequences.fastq.gz>

       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

       Vince Buffalo, https://github.com/vsbuffalo