In the future era of Whole genome sequencing, what will be the role of Sanger sequencing? Does it have any role in epidemiological or phylogenetic studies?
It will surely remain to be useful in many labs that don't have the funds for NGS and as an initial starting point for these types of studies. Lots of labs have genetic analysers and I doubt many of those labs are ready to get rid of them. However, long-term you may be right. With NGS becoming more accessible and affordable (and will soon be the norm), new labs and new studies will likely be driven to explore NGS techniques simply because of the quantity and quality of the data. Thus classical Sanger sequencing may be on borrowed time (it certainly had a good run though).
We still use capillary sequencer in our lab for accurate amplicon length determination, e.g. MLVA-typing & spa typing. Sanger sequencing will remain useful on genome regions with many repetitive elements.
NGS sevres as a toy for scientists, and as a tool for companies who gain all the data in order to use it in future in commercial purposes by means of Sanger sequencing)))
NGS is useful for sequencing genomes or metagenomes. Sanger sequencing is useful for sequencing specific genes and loci. So for the near future is really depends upon the question you are asking and the scale of the project.
From the perspective of a researcher in the field of Virology, i strongly believe that Sanger sequencing will remain a gold standard for confirming the results of NGS. NGS may may be used as a mean to get an information on the viruses present in a given sample, and to develop primers for detailed and reliable sequencing through Sanger.
Definitely have significant role in molecular epidemiological studies, especially related to viruses, where phylogeny reconstruction would need reliable data of sufficient length.
Sanger sequencing still a standard method for DNA sequencing, but the preferred use for rapidly results is the Next-Generation Sequencing (NGS), please see the following link: