MT-Toolbox Files

MTToolbox version 4.1.2

MTToolbox is a set of binaries and libraries for working sequence data that has
been tagged with molecule tags.  Molecule tags are random k-mers that are
attached to individual molecule before PCR and sequencing.  Molecule tags are
useful in reducing PCR bias and seqeuncing error.

After individual DNA molecules are tagged with random k-mers they are PCRed and
sequenced.  By categorizing each of the sequenced reads by their molecule tags
we can correct sequencing errors and reduce PCR bias.  We reduce PCR bias
because if a molecule is preferentially PCRed we can normallize that effect by
colapsing the set of reads with matching molecule tags into one consensus
sequence.  When categorized reads are collapsed into a consensus sequence
errors introduced in the sequencing reaction can be reduced by choosing the most
represented base for each position in the set of categorized reads.

MTToolbox was specifically designed to work with reads from the Illumina MiSeq
mahcine using either single-end (SE), paired-ends (PE) with overlap, or PE
without overlap.  However, in theory it is compatable with other sequencing
technologies and protocols.

For details on installation instructions, descriptions, updates, usage
instructions, and other important information pertaining to MT-Toolbox see:

https://sites.google.com/site/moleculetagtoolbox/home


INSTALLATION

To install this module, run the following commands:

	perl Build.PL
	./Build
	./Build installdeps
	./Build test
	./Build install
	
For more details on installation see:

https://sites.google.com/site/moleculetagtoolbox/installation


REQUIRED DEPENDENCIES

Perl
ClustalW

BioUtils::ConsensusBuilder::ConsensusBuilder
BioUtils::FastaIO
BioUtils::FastqIO
BioUtils::FastqSeq
BioUtils::QC::FastqFilter
BioUtils::SeqSeq::Diagnostics
Carp
Chart::Gnuplot
Class::Std::Utils
Data::Dumper
Exception::Class
File::Basename
File::Spec
File::Temp
Getopt::Long
IPC::Cmd
List::MoreUtils
Math::BigInt
Module::Build
MyX::Generic # Comes with BioUtils
Scalar::Util
Statistics::Descriptive
Storable
Test::Exception
Test::More
Test::Pod
Test::Pod::Coverage
Test::Warn
Tk
Tk::DialogBox
Tk::LabEntry
Tk::NoteBook
XML::Simple
version


OPTIONAL DEPENDENCIES

gnuplot -- needed for building output graphs
FLASH -- needed for overlapping PE reads
X Window System -- needed for using the GUI


LICENCE AND COPYRIGHT

Copyright (c) 2013, Scott Yourstone
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met: 

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   list of conditions and the following disclaimer. 
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   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution. 

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(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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