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Metagenomics Resources
Gavin Douglas edited this page Jan 30, 2018
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Detailed descriptions of Metagenomics processing steps are available on the below pages.
- Please feel free to post a question on the Microbiome Helper google group if you have any issues.
- General comments or inquires about Microbiome Helper can be sent to morgan.langille@dal.ca.
Useful Links
Microbiome Helper 2
- 1.1. Overview - start here!
- 1.2. What you need to start a microbiome analysis
- 1.3. Introduction to command line
- 1.4. Introduction to R and R notebooks
- 1.5. Download tutorial data
- 1.6. Setting up environments for analysis
Microbiome Helper 2 - marker gene/amplicon
Microbiome Helper 2 - metagenome
- 3.1. Metagenomics first steps
- 3.2. Taxonomic annotation with Kraken 2
- 3.3. Functional annotation with MMSeqs 2 (and combining taxonomic and functional annotations)
- 3.4. Getting a tree for metagenomic taxonomic annotations
- 3.5. MAG assembly, binning, and curation with Anvi'o
- 3.6. AMR gene annotation with CARD RGI
- 3.7. Obtaining annotations for function/gene of interest with HMMs
Microbiome Helper 2 - downstream/statistical analysis
Tutorials