A collection of good journal articles related to methods used to study the microbiome. Contributions, in the form of pull requests on the github page are welcome. Please include a description of the paper indicating its importance to the field.
Foundational methods paper describing how to do amplicon sequencing data using paired-end sequencing on the MiSeq.
The ‘kitome’ paper. Why blanks are absolutely essential
Why it’s really not a good idea to ‘rarefy’. Also good evidence for using DESeq2 for identification of differentially abundant OTUs
Note that this is not a list of good blog sites - just single blog posts that are informative and useful
Why do I have such a large distance matrix? - The mothur blog by Pat Schloss link
A rather humorous blog post by Pat Scloss on why you should sequence way more than you think you need, and throw out anything without good quality and overlapping pairs
All of Microbiome Digest is particularly good but here are a couple of useful collections from that website.