Microbial community analysis pipelines in metagenomics
1
0
Entering edit mode
2.3 years ago

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 • 1.1k views
ADD COMMENT
3
Entering edit mode
2.3 years ago

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

ADD COMMENT
0
Entering edit mode

This is great. Many thanks.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1421 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6