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HiTEC: accurate error correction in high-throughput sequencing data
Version 1.0.2: Feb.9, 2011
Copyright 2010 Lucian Ilie, Farideh Fazayeli, Silvana Ilie 
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HiTEC is a C++ program which corrects sequencing errors in high-throughput sequencing data, such as those generated by the Illumina Genome Analyzer. 

Changes made compared to the former version:
-- Removing bugs

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

HiTEC 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 Lesser General Public License for more details: <http://www.gnu.org/licenses/>.


System Requirements
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HiTEC has been tested on systems running Linux on an x86_64 architecture. Compiling the program requires GSL, the GNU Scientific Library (http://www.gnu.org/software/gsl/)


How to install GSL
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1- Download the current stable version of GSL from ftp.gnu.org in the directory /pub/gnu/gsl. (currently we used gsl-1.9)

2- Install GSL

	./configure --prefix= <gslLibrary-PATH>
	make
	make install

It will install GSL in specific path, <gslLibrary-PATH>. Please consult the INSTALL file Installation in gsl directory for more detailed instructions.


How to install HiTEC 
====================

1- gunzip hitecXY.tar.gz (XY = 32 or 64)
	 tar -xvf hitecXY.tar

2- Modify makefile in HiTEC directory in order to set GSL path as installed in your PC

2.a) Set INCLUDEDIRSGSL as
	INCLUDEDIRSGSL = -I<gslLibrary-PATH>/include 
  
  For example, we installed GSL Library in //work/ffazayel/brown/gsl-19 and
	INCLUDEDIRSGSL = I//work/ffazayel/brown/gsl-19/include

2.b)Set LIBDIRS as
	LIBDIRS = -L<gslLibrary-PATH>/lib 
  
  We did
	LIBDIRS = -L//work/ffazayel/brown/gsl-19/lib

3- Compile HiTEC
	make
	
  It will make an exe file in the same directory as HiTEC.



How to run HiTEC
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	./hitec <inputReads> <correctedReads> <GenomeLength> <per-base error rate>

Input Parameters:

<inputReads> - path and name of the input file containing the reads in FASTA or FASTQ format (http://en.wikipedia.org/wiki/FASTQ_format). In the current HiTEC version, reads must be of equal length and contain only the letters {A,C,G,T}.

<correctedReads> - path and name of the output file containing the corrected reads in FASTA format.

<GenomeLength> - length of the genome; if real value is not known, then supply approximate value

<per-base error rate> - error rate x 100; if real value is not known, then supply approximate value


Sample
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For example for the sample dataset it would be

	./hitec S.aureusReads.fasta S.aureusCorrectedReads.fasta 2820462 1


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For any questions, please contact 
Lucian Ilie 
e-mail: ilie@csd.uwo.ca
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