--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nanopolish_index.pl	Mon Feb 12 00:58:10 2018 -0500
@@ -0,0 +1,74 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use 5.012;
+
+use Cwd qw/getcwd abs_path/;
+use File::Copy qw/copy/;
+use Getopt::Long qw/:config pass_through/;
+use threads;
+use threads::shared;
+use BioX::Seq::Stream;
+
+my $fn_link = 'reads';
+
+my $fn_fast5;
+my $fn_reads;
+my $fn_outfile;
+
+# parse genome filename and add back to arg stack
+GetOptions(
+    'fast5=s'   => \$fn_fast5,
+    'reads=s'   => \$fn_reads,
+    'outfile=s' => \$fn_outfile,
+);
+
+my $ret;
+
+$fn_fast5   = abs_path($fn_fast5);
+$fn_reads   = abs_path($fn_reads);
+$fn_outfile = abs_path($fn_outfile);
+
+# extract FAST5 files to path where they are expected
+my $fast5_dir = 'fast5';
+if (-e $fast5_dir) {
+    warn "$fast5_dir exists, won't overwrite";
+    exit;
+}
+mkdir $fast5_dir;
+my $cwd = abs_path( getcwd() );
+chdir $fast5_dir;
+
+# use system 'tar' to transparently and safely handle absolute paths
+$ret = system(
+    'tar',
+    '-xf',
+    $fn_fast5
+);
+die "Failed to extract tarball: $!\n"
+    if ($ret);
+
+chdir $cwd;
+
+symlink( $fn_reads, $fn_link )
+    or die "Failed to create symlink: $@";
+
+# index reads
+$ret = system(
+    'nanopolish',
+    'index',
+    '--directory' => $fast5_dir,
+    $fn_link,
+);
+die "Failed nanopolish indexing: $!\n"
+    if ($ret);
+
+my @idx_fns = glob "$fn_link.*";
+$ret = system(
+    'tar',
+    '-cf' => $fn_outfile,
+    @idx_fns,
+);
+die "Failed tarball creation: $!\n"
+    if ($ret);