Protocols and Data Processing & Analysis Resources
Protocols
Wetlab Protocol:
https://github.com/SchlossLab/MiSeq_WetLab_SOP/blob/master/MiSeq_WetLab_SOP.md
Illumina Recommeded Setup and Sequencing Protocol:
Data Processing:
DADA2
https://benjjneb.github.io/dada2/tutorial.html
Qiime2
https://docs.qiime2.org/2019.1/tutorials/atacama-soils/
Mothur:
https://www.mothur.org/wiki/MiSeq_SOP
Data analysis:
Phyloseq:
https://joey711.github.io/phyloseq/tutorials-index.html
Vegan (R package for data analysis)
https://cran.r-project.org/web/packages/vegan/vignettes/intro-vegan.pdf
Additional Data Analysis Tutorial:
https://grunwaldlab.github.io/analysis_of_microbiome_community_data_in_r/index.html
BIOL701 Microbiomes: Data to Insight - Course by Maggie Wagner and Camille S Delavaux
Biology 202: Ecological Statistics - Course by Tadashi Fukami and Jes Coyle
https://fukamilab.github.io/BIO202/index.html
STAMPS 2018