Question: amplicon sequencing or metagenomics?
gravatar for linnet.roque6
5 weeks ago by
linnet.roque610 wrote:

amplicon sequencing or metagenomics?

What is the difference between the two main methods for studying the microbiome: amplicon sequencing and metagenomic sequencing. What kind of information does each of them provide? What are its advantages, disadvantages and biases?

ADD COMMENTlink modified 5 weeks ago by h.mon30k • written 5 weeks ago by linnet.roque610

One way I approach this is the way NCBI SRA characterizes these terms. Amplicon is classified as strategy in SRA and metagenomic is described as source.

Overall amplicon sequencing is a type of method/assay which not_only but can_also be applied to a sample of type metagenomic.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by microfuge1.8k
gravatar for h.mon
5 weeks ago by
h.mon30k wrote:

I believe what you want to ask is what are the differences and similarities between amplicon sequencing metagenomics vs shotgun metagenomics. There is a good number of papers and posts attempting to answer this question, you can start reading the posts (shorter and simpler):

16S Sequencing vs Shotgun Metagenomic Sequencing

16s vs shotgun

16S sequencing vs. Shotgun metagenomics: Which one to use when it comes to microbiome studies

Metagenomic Shotgun Sequencing

Then move on to some papers, which will provide a more complete view of both techniques, at the expense of being longer, more complex, and harder to read:

Quantitative Assessment of Shotgun Metagenomics and 16S rDNA Amplicon Sequencing in the Study of Human Gut Microbiome

Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by h.mon30k
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