During our first lesson we had a brief overview of the sequencing strategy used for Nannochloropsis.
First, a whole genome shotgun approach was used to have a first draft (see picture below). In particular we used the Roche 454 machine that provides reads ~500bp long, and we assembled them with the Newbler package.
As we saw both read length and sequence coverage affects the quality of the assembly. In particular repeated regions make the assembly program to “break” the sequence. This happens if the length of the repeated region is longer than the single fragments (reads) sequenced. Repeated regions collapse in the same contig, that will have a higher coverage (approximately n-times the average, where n is the number of repeats in the genome).