Is there a way to estimate how large a gap might be after performing 454 pyrosequencing followed by Newbler? I have several closed reference genomes, and I know that my read length is about 400bp with about 40x coverage. Therefore I have high confidence that these gaps are due to repeat regions.
edit I guess this might be answerable by knowing the repeat regions in a genome. How would I identify repeat regions just by the sequence alone? If I knew this length then I would take the repeat region length, L and calculate it by gapLength = L-(2 * 400).