TagCleaner
==========

TagCleaner. For cleaner sequences. (http://tagcleaner.sourceforge.net)

The TagCleaner tool can be used to automatically detect and efficiently remove tag sequences (e.g. WTA tags) from genomic and metagenomic datasets. Go to http://tagcleaner.sourceforge.net/ for access to a user-friendly web-interface, the documentation and the latest updates.TagCleaner will help you to preprocess your genomic or metagenomic sequence data in FASTA or FASTQ format.


STANDALONE VERSION
------------------

The standalone version is a standalone perl script (tagcleaner.pl) that does not require any non-core perl modules for processing.

The used core modules are:
   Getopt::Long
   Pod::Usage
   File::Temp
   File::Path
   Cwd
   Fcntl

To run the standalone version, you can either use "perl tagcleaner.pl [options]" or rename the "tagcleaner.pl" into "tagcleaner", add the execution mode ("chmod +x tagcleaner") and use "tagcleaner [options]".


WEB VERSION - SETUP
-------------------

1. Download the latest version

2. Copy the files to your cgi-bin/ directory

3. Use Firebug (http://getfirebug.com/) to find any other issues such as hard-coded links and change them according to your system setup


WEB VERSION - DEPENDENCIES
--------------------------

The PERL scripts require these modules:

   CGI
   Fcntl
   Data::Dumper
   IO::Uncompress::AnyUncompress


BUG REPORTS
-----------

If you find a bug please email me at <rschmieder_at_gmail_dot_com> so that I can make TagCleaner better.


COPYRIGHT AND LICENSE
---------------------

Copyright (C) 2010-2011  Robert SCHMIEDER

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>.