Below is a collection of useful resources for vairous skills. Most of these are sources I pulled from to create these tutorials. Having a bunch of links means that they will break eventually. If you need them urgently, try googling. Otherwise, let me know to update the links.
EDAMAME was a workshop I went to. The link above is to the schedule, which has tutorials on lots of things including: R, bash, amazon instances, tmux, FileZilla, metagenomics, github, database creation, MOTHUR, and ecological stats. I probably missed a few things. This is a great place to start if you are new. Check out the etherpad on it too!
Phyloseq is the R library you will probably use to analyze and visualize your 16S community data. Look for the tutorials tab on the website.
The people who taught me statistics in R swear by this book. There is also just a plain Numerical ecology version (no R code).
Some people are geniuses, and then there is Jin. Jin is from the GERMS lab at Iowa State and can do anything. He has tons of tools, some of which I have borrowed.
This also has useful scripts that you can borrow, but start with Jin’s github.
Has workflows that may be of use.