Perl script to split a file containing multiple fastq into separate fast files names according to the fast ID

README

SplitFastq.pl is a perlscript written by Joseph Hughes, university of Glasgow

Usage:
  perl SplitFastq.pl -in ourmultifastqfile
  
This script will split a file containing multiple fastq into separate fast files names according to the fast ID.
The script uses Bioperl.

SplitFastq.pl

#!/usr/bin/perl
#

# use this to split a file containing multiple fastq sequences
 
use strict;
use Bio::SeqIO;
use Getopt::Long; 

my ($file);
&GetOptions(
	    'in:s'      => \$file,#file with mutliple fastq 
           );

my $seq_in = Bio::SeqIO->new(-file => $file, -format=> 'fastq');

while( my $seq = $seq_in->next_seq() ) {
  my $id=$seq->id();
  print "ID: $id\n";
  my $outfile=$id.".fastq";
  my $seq_out = Bio::SeqIO->new(-file   => ">$outfile",
                              -format => 'fastq',);
  $seq_out->write_seq($seq);
}