Fundamentals of microbiome study design, sample collection, and data analysis:
- Conducting a microbiome study. Goodrich et al. (2014). Cell 158(2): 250.
- Getting started with microbiome analysis: sample acquisition to bioinformatics. Kumar et al. (2014). Curr Protoc Hum Genet 82: 18.8.1.
Bioinformatics protocols and workflowsfor microbiome and metagenomic studies:
- Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research. Comeau et al.(2017). mSystems 2(1).
- Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses. Callahan et al.(2016) F1000Res 5: 1492.
- An Introduction to QIIME – beginners tutorial for using QIIME for 16S rRNA gene microbial diversity analysis
- PhyloSeq Tutorials – https://joey711.github.io/phyloseq/tutorials-index.html
- Introduction to the microbiome R package – https://microbiome.github.io/tutorials/
- USEARCH v11 manual – https://drive5.com/usearch/manual/ and an open-source alternative https://github.com/torognes/vsearch
- PICRUST – http://huttenhower.sph.harvard.edu/galaxy/
- PIPHILLIN – https://piphillin.secondgenome.com/
- Metagenomic pipeline for profiling the presence/absence of microbial pathways – https://bitbucket.org/biobakery/humann2/wiki/Home
- MetagenomeSeq – https://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html
- Basic data science: Tidyverse – https://www.tidyverse.org/
Microbiome Standards:
- International Human Microbiome Standards (IHMS) project – coordinated development of standard operating procedures designed to optimize data quality and comparability in the human microbiome field
- Minimum information about a metagenome-assembled genome (MIMAG) of bacteria and archaea
- NIH Human Microbiome Project Data Analysis and Coordination Center – central repository for all HMP data
- Earth Microbiome Project – collaborative effort to characterize the planet’s microbial life
- MicrobiomeHD – a standardized database of human gut microbiome studies