--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SeqSero/libs/splitPairedEndReads.pl	Wed Dec 06 15:59:29 2017 -0500
@@ -0,0 +1,21 @@
+use strict;
+use warnings;
+my $file = $ARGV[0];
+open(FILE, "<$file") || die "cannot open $file\n";
+open(OUT1, ">$file\_1") || die "cannot open $file\_1\n";
+open(OUT2, ">$file\_2") || die "cannot open $file\_2\n";
+while(<FILE>){
+    chomp;
+    print OUT1 "$_\/1\n";
+    print OUT2 "$_\/2\n";
+    my $newline = <FILE>; chomp($newline);
+    print OUT1 substr($newline, 0, length($newline)/2)."\n";
+    print OUT2 substr($newline, length($newline)/2, length($newline)/2)."\n";
+    $newline = <FILE>; chomp($newline);
+    print OUT1 "$newline\/1\n";
+    print OUT2 "$newline\/2\n";
+    $newline = <FILE>; chomp($newline);
+    print OUT1 substr($newline, 0, length($newline)/2)."\n";
+    print OUT2 substr($newline, length($newline)/2, length($newline)/2)."\n";
+}
+close(FILE);