Microbial community analysis pipelines in metagenomics

Question

[ramin.k2013]

I want to research about existing microbial community analysis and taxonomic profiling pipelines for metagenomics data like MetaPhlan3 or Kraken2. Is there any review published so I can start doing research? I can not find one and I do not know the major pipelines in the field for metagenomics data. Is there any source or links regarding any of the existing taxonomic profiling pipelines to put me on the track?

Answer 1

[Bertalan_Takacs]

I am working currently on very similar things and finding this article was a huge help for me. https://www.sciencedirect.com/science/article/pii/S0092867419307755?via%3Dihub#sec1

If you want to try an integrated pipeline for metagenomic analysis, Sunbeam has worked great for me in the past. https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0658-x

[ramin.k2013]

This is great. Many thanks.

[Kumar]

I am wondering why you did not find useful MetaPhlan3 or Kraken2 and looking for something new.

[ramin.k2013]

I just want to see what is out there and what are the pros and cons before using the pipeline for my project.