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:

https://support.illumina.com/documents/documentation/chemistry_documentation/16s/16s-metagenomic-library-prep-guide-15044223-b.pdf

 

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

https://osf.io/uwg7x/

Biology 202: Ecological Statistics - Course by Tadashi Fukami and Jes Coyle

https://fukamilab.github.io/BIO202/index.html

STAMPS 2018

https://github.com/mblstamps/stamps2018/wiki

Resources & Opportunities