N50 = length-weighted median.: The size of the smallest contig such that 50% of the length of the genome is contained in contigs of size N50 or greater.

N90 is 90%.

If you have done the assembly work, and you have got the contigs in FASTA format, it is easy to calculate the N50 & N90 contig size, for example:

Code:

perl -e 'my ($len,$total)=(0,0);my @x;while(<>){if(/^[\>\@]/){if($len>0){$total+=$len;push@x,$len;};$len=0;}else{s/\s//g;$len+=length($_);}}if ($len>0){$total+=$len;push @x,$len;}@x=sort{$b<=>$a}@x; my ($count,$half)=(0,0);for (my $j=0;$j<@x;$j++){$count+=$x[$j];if(($count>=$total/2)&&($half==0)){print "N50: $x[$j]\n";$half=$x[$j]}elsif($count>=$total*0.9){print "N90: $x[$j]\n";exit;}}' contigs.fa