TagCleaner Files

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 report it at http://groups.google.com/group/EdwardsLabTools/ so that we can make TagCleaner better.


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

Copyright (C) 2010-2013  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/>.


VERSION HISTORY
---------------

Certain updates only apply to the web version, but they should be obvious to
figure out since they are likely modification of the interface.

tagcleaner-standalone-0.16:
Support tag prediction in mixed-case sequences.

tagcleaner-standalone-0.15:
Fix warnings during tag prediction.

tagcleaner-standalone-0.14:
Fixed issue with line width parameter not being set. Fix warnings with
defined statements.

tagcleaner-standalone-0.13:
Fixed issue that generated warnings when the trimmed sequence is zero-length.
Modified filename check to prevent endless loop. Other minor fixes.

tagcleaner-web-0.12 / tagcleaner-standalone-0.12:
Added matrix "exact" to allow trimming of ambiguous bases without considering
the ambiguity code.

tagcleaner-web-0.11.1 / tagcleaner-standalone-0.11.1:
Corrected typo in regex (missing \ before s*).

tagcleaner-web-0.11 / tagcleaner-standalone-0.11:
Added support for ambiguous characters in the input sequences (thanks to Dave
Messina from Stockholm for the suggestion). Character matching can be set based
on three predefined matrices (new option -matrix). Non-IUPAC characters for
nucleic acids are mismatched by default.

tagcleaner-web-0.10 / tagcleaner-standalone-0.10:
Fixed issue in tag detection for unknown shifts. Added File::Path for legacy
support.

tagcleaner-web-0.9 / tagcleaner-standalone-0.9:
First release of standalone version. Web version now uses standalone version in
backend. Improved tag detection. New features for the splitting of concatenated
fragments and tag repeats. Filter options are now limited as filtering should be
performed using PRINSEQ tool after trimming. Web version now allows FASTQ input
and output and the processing of larger input files.

tagcleaner-web-0.8:
Fixed issue with uninitialized qual variable causing silent errors. Fixed issue
with "good"/"bad" in output selection. Fixed issue with undefined header line.

tagcleaner-web-0.7:
Fixed bug in tag detection when no shifts can be found. Fixed issue in parsing
FASTQ files with no information in '+' header line.

tagcleaner-web-0.6:
Added new function to tag sequence detection interface: "Use as 3'-end". Added
Javascript function to check for tag sequence length to restrict tag sequences
to max 64 bp.

tagcleaner-web-0.5:
Fixed "substr outside of string" during detection of tag sequence repeats.

tagcleaner-web-0.4:
Fixed cross browser issues. Added new functions to tag sequence detection
("Reset to prediction" and "Clear all").