I'd personally go for Next-Gen sequencing. It's a bit more prep work, but is almost always cheaper in the long run. Also, PCR is biased by primer selection & amplification efficiency. You'll get a mixed sample of amplified genes so you'll either need to use NGS anyway or spend a ton of time cloning and sequencing.

Good luck!

Hi, Katie A Burnette ,

Thank you for your response. To shed more context, my research primarily aims to catalog ARGs present in water sources and distribution systems of a major region in my country. I read papers that employed one of the methods and other papers employing both.

Originally, I would be employing NGS + bioinformatic analysis to detect ARGs or ARG-like sequences from my metagenome data. However, one concern arising from this is low copies of ARGs/ARG-like sequences that may lead to underdetection/non-detection. This is the reason why I am thinking about adding PCR amplification of expected ARGs. But since my work would be the first to catalog ARGs from water sources and distribution systems of my chosen research locale (to my knowledge), I don't have any basis in selecting which ARGs to amplify. Do you think combining both techniques is a good option?

-Arizaldo

Next gen is better

Thank you, Asemoloye Micheal Dare .

We would probably recommend NextGen sequencing as it would provide unbiased coverage from all species present in your samples.

Arizaldo Castro , check the publication dates on the prior studies. If they are more than 5 years old, they are out of date as far as sequencing technology. If you have to choose, do the NGS only. If you have the time & money, do NGS and PCR. You can compare & contrast the two methods. I'd pick ARGs that are previously published and ones for loci that you predict could be interesting for your sampling location.

Thank you, Richard Casey .