IllQ2SanQ.pl

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#!/usr/bin/perl -w

# AUTHOR: Joseph Fass
# LAST REVISED: August 2009
# 
# The Bioinformatics Core at UC Davis Genome Center
# http://bioinformatics.ucdavis.edu
# Copyright (c) 2009 The Regents of University of California, Davis Campus.
# All rights reserved.

# IllQ2SanQ.pl converts Illumina (>= 1.3 pipeline) fastq format to Sanger fastq format

while (<>) {
	$head1 = $_;
	$seq = <>;
	$head2 = <>;
	$qual = <>;
	print $head1.$seq.$head2;
	chomp $qual;
	@Q = split(//,$qual);
	for ($i=0; $i<=$#Q; $i++) {
		print chr( ord($Q[$i]) - 31 );
	}
	print "\n";
}