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Old SOPs
Robyn Wright edited this page Sep 19, 2025
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Please note that current SOPs are in the main sidebar for this Wiki.
- 16S Bacteria/Archaea SOP v1
- 18S Eukarya SOP v1
- ITS2 Fungi SOP v1
- 16S/18S/ITS SOP v1 Detailed Resources
- PacBio Amplicon SOP v1
- Amplicon SOP v2 (qiime2 2018.6)
- Amplicon SOP v2 (qiime2 2018.8)
- Amplicon SOP v2 (qiime2 2019.7)
- Amplicon SOP v2 (qiime2 2019.10)
- Amplicon SOP v2 (qiime2-2020.8)
- Amplicon SOP v2 (qiime2-2022.11)
- Amplicon SOP v2 (qiime2-amplicon-2024.5)
- PacBio Amplicon SOP v2 (qiime2-2022.2)
- Amplicon SOP v2 (virtual box workflow)
- 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