#THIS DOESN'T READ THE FILE RIGHT.. my $file = "Qual.txt"; my $qual_obj = Bio::SeqIO->new(-file =>"<$file",-format=>'fasta',); my %seq_hash = (); while(my $seq= $qual_obj->next_seq){ $seq_hash{$seq->id} = $seq->seq; } use Data::Dumper; print Dumper(\%seq_hash);