use strict;
my $str = 'NF3-9-16S_S9_1456|M02255:210:000000000-B9K3P:1:1101:14397:18152 1:N:0:9|o:50|m/o:0.720000|MR:n=0;r1=34;r2=2|Q30:p=97;p=100|CO:0|mismatches:36
NF3-9-16S_S9_9999|M02255:210:000000000-B9K3P:1:1101:14397:18152 1:N:0:9|o:50|m/o:0.720000|MR:n=0;r1=34;r2=2|Q30:p=97;p=100|CO:0|mismatches:36';
my $regex = qr/NF.*?(\d*)\|.*/p;
my $subst = 'Re1_91910_$1';
my $result = $str =~ s/$regex/$subst/rg;
print "The result of the substitution is' $result\n";
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for Perl, please visit: http://perldoc.perl.org/perlre.html