<p>Several pieces of software require this parameter.</p>

<p>Is counting the number of masked nucleotides in fasta files going to give a good approximate result?</p>

<p>If not, is there a simple way to do it?</p>

<p><strong>EDIT:</strong> if you understand effective genome size as &quot;mappable&quot; genome size, than Devon is right, of course.</p>

<p>Assemblies only will provide you with a good size estimate if they are of really high quality. This is usually only the case for either model organisms or small, bacterial genomes.</p>

<p>Assemblies of larger genomes such as plant, animals etc., and in particular draft genomes usually do not contain a complete representation of a single haplogenome - which you would need to get your size estimate right. The reasons are that assembly algorithms usually cannot resolve all repeats and centromeric/telomeric regions, and also are prone to generate multiple sequences for different alleles of the the same region.</p>

<p>In my opinion, there are two better approaches:</p>

<p>1) Use the experimentally determined nuclear DNA (e.g. <a href="http://www.genomesize.com/">www.genomesize.com</a>) content to calculate the haploid genome size. DNA content in pg can be directly converted into a bp estimate.</p>

<p>2) Use a k-mer based approaches to estimate the genome sizes form a high coverage NGS data set of your organism</p>
