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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" PRINSEQ \- PReprocessing and INformation of SEQuence data .SH "VERSION" .IX Header "VERSION" PRINSEQ-graphs 0.6 .SH "SYNOPSIS" .IX Header "SYNOPSIS" perl prinseq\-graphs.pl [\-h] [\-help] [\-version] [\-man] [\-verbose] [\-i input_graph_data_file] [\-png_all] [\-html_all] [\-log file] .SH "DESCRIPTION" .IX Header "DESCRIPTION" \&\s-1PRINSEQ\s0 will help you to preprocess your genomic or metagenomic sequence data in \s-1FASTA\s0 (and \s-1QUAL\s0) or \s-1FASTQ\s0 format. The graphs version allows users of the lite version to generate graphs similar to the web version. .SH "OPTIONS" .IX Header "OPTIONS" .IP "\fB\-help\fR | \fB\-h\fR" 8 .IX Item "-help | -h" Print the help message; ignore other arguments. .IP "\fB\-man\fR" 8 .IX Item "-man" Print the full documentation; ignore other arguments. .IP "\fB\-version\fR" 8 .IX Item "-version" Print program version; ignore other arguments. .IP "\fB\-verbose\fR" 8 .IX Item "-verbose" Prints status and info messages during processing. .IP "\fB***** \s-1INPUT OPTIONS\s0 *****\fR" 8 .IX Item "***** INPUT OPTIONS *****" .PD 0 .IP "\fB\-i\fR " 8 .IX Item "-i " .PD Input file containing the graph data generated by the lite version. .IP "\fB***** \s-1OUTPUT OPTIONS\s0 *****\fR" 8 .IX Item "***** OUTPUT OPTIONS *****" .PD 0 .IP "\fB\-o\fR " 8 .IX Item "-o " .PD By default, the output files are created in the same directory as the input file with an additional \*(L"_prinseq_graphs_XXXX\*(R" in their name (where \s-1XXXX\s0 is replaced by random characters to prevent overwriting previous files). To change the output filename and location, specify the filename using this option. The file extension will be added automatically. .IP "\fB\-png_all\fR" 8 .IX Item "-png_all" Use this option to generate \s-1PNG\s0 files with the graphs. .IP "\fB\-html_all\fR" 8 .IX Item "-html_all" Use this option to generate a \s-1HTML\s0 file with the graphs and tables. .IP "\fB\-log\fR " 8 .IX Item "-log " Log file to keep track of parameters, errors, etc. The log file name is optional. If no file name is given, the log file name will be \*(L"inputname.log\*(R". If the log file already exists, new content will be added to the file. .SH "AUTHOR" .IX Header "AUTHOR" Robert \s-1SCHMIEDER,\s0 \f(CW\*(C`\*(C'\fR .SH "BUGS" .IX Header "BUGS" If you find a bug please email me at \f(CW\*(C`\*(C'\fR or use http://sourceforge.net/tracker/?group_id=315449 so that I can make \s-1PRINSEQ\s0 better. .SH "COPYRIGHT" .IX Header "COPYRIGHT" Copyright (C) 2011\-2012 Robert \s-1SCHMIEDER\s0 .SH "LICENSE" .IX Header "LICENSE" This program is free software: you can redistribute it and/or modify it under the terms of the \s-1GNU\s0 General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. .PP This program is distributed in the hope that it will be useful, but \s-1WITHOUT ANY WARRANTY\s0; without even the implied warranty of \s-1MERCHANTABILITY\s0 or \s-1FITNESS FOR A PARTICULAR PURPOSE.\s0 See the \s-1GNU\s0 General Public License for more details. .PP You should have received a copy of the \s-1GNU\s0 General Public License along with this program. If not, see .