Does something like this fit in memory with your data?

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1169599

use strict;
use warnings;

my @data = 1..6e4;         # fake strings
my @rows = 1+3e4..6e5+3e4; # fake strings

my %combined;
@combined{@data, @rows} = ();

@data = keys %combined;

print "size = " . @data, "\n";
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