In 16s rDNA metagenome analysis, after sequencing data. I want to classify bacteria based on their functions. I am looking for a Pipeline or any software that can do this job?
I hope these Article A review of methods and databases for metagenomic classifica...
Article INVITED REVIEW: Microbial ecology in the age of genomics and...
will interest you.
Article Characterization of the Gut Microbiome Using 16S or Shotgun ...
https://academic.oup.com/nar/article-pdf/48/16/e93/33746402/gkaa568.pdf
Article Microbial resolution of whole genome shotgun and 16S amplico...
PICRUSt2 and Tax4Fun are the two most common pipelines used for functional predictions based on 16s sequencing data.
These can be run in QIIME or else you can also use them through the web based MicrobiomeAnalyst tool
https://doi.org/10.1038/s41596-019-0264-1
https://www.microbiomeanalyst.ca/
These resources might help you.
Good luck
Thank you all for your response.
Muhammad Ali The provided reviews are helpful for analyzing the metagenome data but they are not providing the answer to my question. Thank you
Aravinda C V thank you for your files. Nazima Habibi Thank you for your suggestion. I have already tried PICRUSt and Tax4fun. In these based on OTUs, they are providing the metabolism gene and their abundance. But, my question is different, that is
In 16s sequencing but not shotgun sequencing, After obtaining the contigs with their representative OTUs followed by taxonomical bacterial classification. Based on the function of bacteria like specific metabolite producing bacteria (example: Methane producing bacteria, Nitrogen-fixing bacteria, vitamins producing bacteria) classification and the list of bacteria followed by their abundance is what, I am looking for?
Please let me know, if any pipeline can do this job.... Thank you
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