Abstract
Shotgun sequencing has been widely used to determine the sequence of a long segment of DNA or even the whole genome. Short DNA reads need to be reconstructed into long sequences using assembly programs. Ultimately one should end up with a single long contig for each single DNA molecule or each chromosome in terms of an entire genome. However, in practice, this is very difficult due to repetitive DNA sequences. Usually, repetitive reads are not used in assembly. Thus, several contigs will be present in the 'final asssembly'. In my talk, I'll present a method to make use of those repetitive reads to close gaps. Basically, we used forward-reverse clone constraints to identify potential repetitive reads which fall in a gap, and then do a mini-assembly for the small set of DNA reads. By this means, we can get longer contigs and fewer gaps.