In every method of genome sequencing, identifying the existence of duplicate regions is not very easy. In the whole genome, shotgun method is less effective than clone based method for finding such regions. By the whole genome shotgun method, we can easily access to the suspected clones, which are useful for further analysis.
Comparative genomic hybridization is an effective method. It has been proved more effective than genomic sequencing.
The clone based approach is less likely to make mistakes when long shotgun fragments are used. Also, the chromosomal location for each BAC is known. But this takes time and is also expensive.
The whole genome shotgun method is faster and less expensive but more prone to mistakes. If a 100 Kb part of a chromosome is duplicated and each strand is cut into small fragments of size 2 Kb, it would be difficult to find out where a specific 2 Kb piece is located in the sequence.
Hence, the best method would be comparative genomic hybridization.