.TH "SCYTHE" "1" "May 2015" "Vince Buffalo" "scythe"
.
.SH "NAME"
\fBscythe\fR \- Bayesian adaptor trimmer
.
.SH "SYNOPSIS"
scythe \-t sanger \-a /path/to/adaptors\.fasta [options] <sequences\.fastq\.gz>
.
.P
Trim 3\'-end adaptor contaminants off sequence files\. If no output file is specified, scythe will use stdout\.
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.SH "OPTIONS"
.
.nf
 \-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

.nf
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]
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.SH "FILES"
.nf

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.
.SH "AUTHOR"
Vince Buffalo, https://github.com/vsbuffalo