The following article is written with excerpts from the second edition of The Sequencing Buyer’s Guide, written by Professor David Smith of the Mayo Clinic in Rochester, NY.
Massively parallel sequencing (MPS) is a high-throughput method to determine a portion of the nucleotide sequence of an individual’s genome. It uses next generation sequencing technologies that are capable of processing multiple DNA sequences in parallel. 
In our “Sequencing Buyer’s guide”, many commercial MPS platforms were reviewed with what they can be used for. In one of his final chapters, he discusses “How to choose which MPS approach is best for your needs” and a series of questions you will need to ask yourself, a summary of which can be found here:
Can your institution afford the full cost of MPS capabilities?
One thing David doesn’t recommend is buying your own sequencer. The best place to set up MPS is in a Core Laboratory. The full cost of MPS includes setting up the infrastructure for utilising MPS within your institution, including personnel with the expertise in the preparation of various libraries prior to sequencing.
A major, but often overlooked aspect of MPS is the need for a wide range of bioinformatic expertise, a single token bioinformatician will not be able to do it. How extensively will your institution need to hire new staff to meet this need?
What does your institution plan to use MPS for?
Very few places will want to do one type of MPS, thus, how many MPS applications will your Core Laboratory need to be running? Different applications have ideal instruments and different providers and if you do not have the funds available to fully develop MPS technologies, some providers offer small devices that can offer an individual lab the opportunity to develop long read sequence data without large instrument purchase prices.
Does your institution have the capability to store the data you will be generating?
MPS will produce a massive amount of data. Do you have the capabilities to store this data?
Before you buy any instrumentation, remember the lifespan.
You must consider the life span of the instrumentation before a newer and higher throughput instrument is developed. It costs a lot of money just to start setting up MPS at a place that does not have the capabilities and it would require additional money on a yearly basis.
Have you considered sending your necessary nucleic acids for external analysis?
This may be the most cost-effective solution if your institution does not have the funds to set up MPS correctly. However, David suggests that MPS is too essential moving forward for institutions not to consider getting into this field, and even if your institution does have a set up using MPS, it may not hold the instruments for a specific application
If your institution does not have a large budget to set up MPS, you need to understand and decide what the major uses of MPS is for your community and meet those needs. If your institution decides to invest in an MPS set up, you can read our full sequencing buyers guide with a review of technologies here.