Helicos: "dark nucleotides" and the coverage parameter

[Irina Pulyakhina]

Dear Mosaik users,

I'm quit new to this program. I work with the Helicos data so it's crucial for me to know the following: aligning the Helicos data to the reference genome sequence, does Mosaik take the coverage meaning into consideration?

Thanks in advance!

Cheers,
Irina