Introduction
Requirements
1. Combine all taxonomic annotations
1.1. Collate all annotations for each read for each sample
Only necessary if you have used our two-step classification system (and want taxonomic classifications from more than one source!) Read-by-read for each sample
1.2. Choose preferred annotation for each read for each sample
2. Combine all functional annotations
Only necessary if you want functional annotations from more than one source!
3. Create normalised taxa + function tables
3.1. Prepare a master input file
3.2. Generate the final normalized tables
Note that this differs from what was here previously as the script now generates these all at once, instead of needing to be re-run multiple times.
4. Append functional descriptions
5. Generate pathway information
6. Visualisation with JarrVis
Authors: Robyn Wright, Dhwani Desai, Gina Filloramo, André Comeau
First created: 13 July 2021
Last updated: 16 October 2026
Based on initial versions by: André Comeau (Metagenomics Standard Operating Procedure v3) and Robyn Wright (Microbiome Helper 2 Annotation of reads with MMSeqs2)
