Split fastq mates

Here is code in perl to split a single paired interleaved FASTQ file into a pair of FASTQ files:

#!/usr/local/bin/perl -w
# Daniel Brami
# Util to split interlaced FASTQ files into pairs

use strict;

# Standard lib
use IO::File;
use File::Basename;

my $INPUT=shift;

if (!(defined ($INPUT)) || ($INPUT =~ '^\-')){
die "Usage: $0 <interleaved paired FASTQ file>\n";
}

my ($name,$path,$suffix) = fileparse($INPUT, qw/fastq FASTQ txt TXT/);

my $FH_IN = new IO::File($INPUT, "r") or die "could not open $INPUT: $!\n";
my $FH_OUT1 = new IO::File($name."split1.$suffix", "w") or die "could not open $name.split1$suffix for writing: $!\n";
my $FH_OUT2 = new IO::File($name."split2.$suffix", "w") or die "could not open $name.split2$suffix for writing: $!\n";

my ($recs1, $recs2)= (0,0);
my $flipflop = 1;
my $counter = 0;
my ($line, $TXT);
while($line = $FH_IN->getline()){
$TXT .= $line;
$counter++;
if($counter == 4){
 if($flipflop == 1){
  print $FH_OUT1 $TXT;
  ++$recs1;
 }else{
  print $FH_OUT2 $TXT;     
  ++$recs2;
 }
 $counter = 0;
 $TXT = '';
 $flipflop *= -1;
}
}
$FH_IN->close();
$FH_OUT1->close();
$FH_OUT2->close();

print STDERR "Processed $recs1 records for pair file 1 and $recs2 records for pair file 2.\n";
if($recs1 != $recs2){
print STDERR "The number of processed records does not match - check input data!";
}exit;

Quality trimming fastq files using CLC Bio cell

1. copy the mandatory license.properties file to your working directory
2. /usr/local/packages/clc-ngs-cell/quality_trim -o -p -c -l -m -r -i &
3. Optional: Split the resulting interleaved paired file into two components:
   ~/workspace/meta_scripts/splitMatedFastq.pl