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Blog:97 Different Ways to do Metagenomics Classification...
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14 months ago
Rockville, MD

Hey all - I’ve notice a lot of people asking “how do i do X” wrt metagenomics or microbiome profiling. Or similarly- “Whats the best database / method / approach / etc?” for metagenomics. The reality is that it depends... on your specific research question, and on the underlying database you want / need to use. Etc.

So - I just wanted to share here something I’ve been curating for the last few years. I have been collecting papers on various pipelines for metagenomics analysis - species/strain ID, functional characterisation, etc. and the number is quickly approaching 100+ (i expect it will be by the end of the month)

https://microbe.land/2018/12/13/97-metagenomics-classifiers/

If I’ve missed a paper - please let me know. The main focus here is on methods papers, not primary (wet lab) research papers - there would be far more...

I’ve also created a Zotero group to track these so I’ll be updating it as well (link is in the post) - which may make it easier to use these citations in your own research / manuscripts / etc. (if you use Zotero)

Hope someone finds this useful.

Thanks - j

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For general information, blog/ website is about 97 publications for various methods used in data analysis, not links to tools for classifying metagenome data.

For eg. doi: https://doi.org/10.1186/s12864-016-3254-5 points to "Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis" manuscript.

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Thanks for the clarification. Also - here’s a direct link to the Zotero repo I have with the citations

https://www.zotero.org/groups/2255187/microbial_genomics_references/items?

(which i believe should include links to the articles and ability to download as bibtex, etc)

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