Initial commit

separate_readpairs.pl

@@ -0,0 +1,19 @@
+#!/usr/local/bin/perl -w
+
+my $in=$ARGV[0];
+open(IN, "<$in");
+open(OUT1, ">forward.fastq");
+open(OUT2, ">backward.fastq");
+my $count = 0;
+while(<IN>) {
+  if ($count < 4) {
+    print OUT1 $_;
+  } else {
+    print OUT2 $_;
+  }
+  $count++;
+  if ($count == 8){ $count = 0;}
+}
+close(IN);
+close(OUT1);
+close(OUT2);