- Intro to Amplicon Sequencing Presentation (PDF)
- 2024 presentations PDF files (need PSU authentication to access)
Weinroth MD, Belk AD, Dean C, et al. Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies. J Anim Sci. 2022;100(2):skab346. doi:10.1093/jas/skab346 Link
Ginnan N, Bordenstein SR. It is time to authenticate the Microbiome Sciences with accredited educational programs and departments. PLoS Biol. 2023 Dec 7;21(12):e3002420. doi: 10.1371/journal.pbio.3002420. PMID: 38060452; PMCID: PMC10703218. Link
Mirzayi C, Renson A; Genomic Standards Consortium; Reporting guidelines for human microbiome research: the STORMS checklist Nat Med. 2021 Nov;27(11):1885-1892. doi: 10.1038/s41591-021-01552-x. Epub 2021 Nov 17. PMID: 34789871; PMCID: PMC9105086.Link
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581-583. doi:10.1038/nmeth.3869 Link
Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome Datasets Are Compositional: And This Is Not Optional. Front Microbiol. 2017;8:2224. Published 2017 Nov 15. doi:10.3389/fmicb.2017.02224 Link
Software: R and Rstudio
Packages: dada2 , phyloseq, and tidyverse
Link to an overview of sequencing methodologies
Link to an overview of bioinformatics
It is great to start grappling with concepts - videos are short
https://www.coursera.org/lecture/microbiome/welcome-to-the-course-AuMZk
For getting used to best practices in coding in the command line
https://www.biostarhandbook.com/index.html
Before you do biostars handbook do this quick shell one https://swcarpentry.github.io/shell-novice/
Riffomonas has great tutorials to get started with R and reproducible research with version control is also a must. https://riffomonas.org/
16S analysis in R
https://benjjneb.github.io/dada2/tutorial.html
16S analysis in Qiime2
https://docs.qiime2.org/2021.11/tutorials/overview/