Any strategy chosen to complete a large-scale sequencing project has pros and cons.
Some groups strongly favor a directed over a shotgun sequencing strategy, while others strongly support the opposite approach. A shotgun strategy typically follows the completion of a high resolution physical map and allows rapid accumulation of data with high redundancy. A primer-walking strategy does not require multiple clonings or template preparations and produces minimally redundant sequence information. The primary disadvantages of primer walking include the cost of synthesizing new primers to extend the sequence and the delay in synthesizing these new primers. Strategies for high-volume sequencing using a primer library composed of short oligonucleotides sufficient to prime multiple DNA sequencing reactions are being developed.