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Microbial community analysis pipelines in metagenomics

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?

metagenomics kraken2 metaphlan3
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updated by Ram Ram • written by ramin.k2013 • ramin.k2013

1 answer

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

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written by Bertalan_Takacs • Bertalan_Takacs

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

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written by Kumar Kumar

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

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written by ramin.k2013 • ramin.k2013

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