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commit 8d5d44b510d1fa253d6fab30ef59e650c0a9ea7f Author: Kevin Murray <[email protected]> Date: Mon May 11 17:06:21 2015 +1000 Add hand-made scythe.1 manpage --- debian/scythe.1 | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/debian/scythe.1 b/debian/scythe.1 new file mode 100644 index 0000000..1503e01 --- /dev/null +++ b/debian/scythe.1 @@ -0,0 +1,41 @@ +.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 adapter contaminants off sequence files\. If no output file is specified, scythe will use stdout\. +. +.SH "USAGE" +. +.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 +. +.SH "Quality Schemes" +.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] +. +.SH "AUTHOR" +Vince Buffalo, https://github.com/vsbuffalo -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/scythe.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
