http://wiki.bits.vib.be/index.php/Identify_the_Phred_scale_of_quality_scores_used_in_fastQ

#  S - Sanger        Phred+33,  raw reads typically (0, 40)#  X - Solexa        Solexa+64, raw reads typically (-5, 40)#  I - Illumina 1.3+ Phred+64,  raw reads typically (0, 40)#  J - Illumina 1.5+ Phred+64,  raw reads typically (3, 40) with 0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold)#  L - Illumina 1.8+ Phred+33,  raw reads typically (0, 41)

　　

一个Perl脚本

#!/usr/bin/perl -w# http://wiki.bits.vib.be/index.php/Identify_the_Phred_scale_of_quality_scores_used_in_fastQuse strict;use File::Basename;use List::MoreUtils qw( minmax );# fastq_detect.pl fastq.file sample-size# detect fastQ format from quality scores in fastQ input file# Version 3## Stephane Plaisance - VIB-BITS - July-04-2012# Joachim Jacob - Aug-02-2012 - joachim.jacob@gmail.com# - changed the maximum value of Sanger to 73# - changed reading the file with a file handle#   (was a file handle !! supporting several archive formats. SP)# - changed the diagnosing algoritm# Stephane Plaisance - VIB-BITS - April-08-2013# - merged both versions and corrected flaw in min/max# thanks to Sergey Mitrfanov for perl reformatting###################################################################### diagnose#   SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS.....................................................#   ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......................#   ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII......................#   .................................JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ......................#   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL....................................................#   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~#   |                         |    |        |                              |                     |#  33                        59   64       73                            104                   126# S 0........................26...31.......40# X                          -5....0........9.............................40# I                                0........9.............................40# J                                   3.....9.............................40# L 0.2......................26...31........41##  S - Sanger        Phred+33,  raw reads typically (0, 40)#  X - Solexa        Solexa+64, raw reads typically (-5, 40)#  I - Illumina 1.3+ Phred+64,  raw reads typically (0, 40)#  J - Illumina 1.5+ Phred+64,  raw reads typically (3, 40) with 0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold)#  L - Illumina 1.8+ Phred+33,  raw reads typically (0, 41)#####################################################################my $script = basename($0);@ARGV gt 0 or die "usage: $script 
      
      
       \n";my ($inputfile, $limit) = @ARGV;if (! defined $limit) { $limit = 100}; # check first 100 recordsmy $cnt=0;my ($min, $max); # global min and max values# print STDERR "\n## Analysing ".$limit." records from $inputfile ... \n";my $z = ReadFile ($inputfile) || die "Error: cannot read from variant file $inputfile: $!\n";## parsewhile (my $id = <$z>) {	$id =~ m/^@/ || die "expected @ not found in line 1!\n";	my $seq = <$z>;	my $sep = <$z>;	$sep =~ m/^\+/ || die "expected + not found in line 3!\n";	my $qual = <$z>;	chomp($qual);	$cnt++;	$cnt>=$limit && last;	# char to ascii	my @chars = split("", $qual);	my @nums = sort { $a <=> $b } (map { unpack("C*", $_ )} @chars);	if ($cnt==1) {		($min, $max) = minmax @nums;	} else {		my ($lmin, $lmax) = minmax @nums; # local values for this read		$lmin<$min ? $min=$lmin : $min=$min;		$lmax>$max ? $max=$lmax : $max=$max;	}}undef $z;## diagnosemy %diag=(			'Sanger'		=> '.',			'Solexa'		=> '.',			'Illumina 1.3+'	=> '.',			'Illumina 1.5+'	=> '.',			'Illumina 1.8+'	=> '.',			);my %comment=(			'Sanger'		=> 'Phred+33,  Q[33; 73],  (0, 40)',			'Solexa'		=> 'Solexa+64, Q[59; 104], (-5, 40)',			'Illumina 1.3+'	=> 'Phred+64,  Q[64; 104], (0, 40)',			'Illumina 1.5+'	=> 'Phred+64,  Q[66; 104], (3, 40), with 0=N/A, 1=N/A, 2=Read Segment Quality Control Indicator',			'Illumina 1.8+'	=> 'Phred+33,  Q[33; 74],  (0, 41)',			);if ($min<33 || $max>104) { die "Quality values corrupt. found [$min; $max] where [33; 104] was expected\n"; }if ($min>=33 && $max<=73)  {$diag{'Sanger'}='x';}if ($min>=59 && $max<=104) {$diag{'Solexa'}='x';}if ($min>=64 && $max<=104) {$diag{'Illumina 1.3+'}='x';}if ($min>=66 && $max<=104) {$diag{'Illumina 1.5+'}='x';}if ($min>=33 && $max<=74)  {$diag{'Illumina 1.8+'}='x';}## report# print STDERR "# sampled raw quality values are in the range of [".$min."; ".$max."]\n";# print STDERR "# format(s) marked below with 'x' agree with this range\n";foreach my $format (sort keys %diag) {	#print STDERR sprintf("  %-13s : %2s  [%-30s] \n", $format, $diag{$format}, $comment{$format});	if ($diag{$format} eq "x") {print "$format\n"}}################## Subs ##### reads from uncompressed, gzipped and bgzip fastQ filessub ReadFile {	my $infile = shift;	my $FH;	if ($infile =~ /.bz2$/) {		open ($FH, "bzcat $infile |") or die ("$!: can't open file $infile");	} elsif ($infile =~ /.gz$/) {		open ($FH, "zcat $infile |") or die ("$!: can't open file $infile");	} elsif ($infile =~ /.fq|.fastq|.txt$/) {		open ($FH, "cat $infile |") or die ("$!: can't open file $infile");	} else {		die ("$!: do not recognise file type $infile");	}	return $FH;}