My undergraduate thesis partner and I will be identifying and characterizing the microbial diversity in 3 sample sites from an urban river. We were thinking of using Sanger sequencing since we would just like to identify what is in the river, but NGS yields a lot of data to really characterize the bacteria present. Our main issue with NGS however would be cost. We are planning to apply for subsidies but our budget is around PHP 20,000 or USD 360. If we will be sending 3 samples, which institution has the most affordable NGS sequencing service? What are possible alternatives to NGS that are more cost-friendly to undergraduate students?
Hi, without sounding too negative, $360 is not going to be sufficient for any NGS runs. Either do Sanger, or 1) apply for smaller funds at your university, 2) talk to a PI who works in this area and ask whether you could add your samples to their NGS runs for free and use 1-2% of their outputs, 3) 16S microarray might be cheaper but not very widespread, will be more difficult to analyze but if you have a local microarray lab, it may be doable.
Also, depending on what diversity you would like to analyze, consider phylum-level qPCRs if it fits your project goals.
Péter Gyarmati if we choose to do Sanger, are there any additional steps that need to be done to get as much data as possible?
For Sanger, you need a purified PCR product. I am not sure what you mean by as much data as possible - you will get a single consensus sequence for each direction up to ~800 base. I would recommend talking to a sequencing lab or whoever has a sequencing machine at your university to discuss your options.
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