Index

Below is a complete index of all pages available on this website.

• Cheatsheet

• Introduction: What is the microbiome?

• SOP: Bioinformaticians start here

• SOP: Downstream analysis

• SOP: Marker gene workflow

• SOP: Metagenome

• SOP: Metagenome 1 - Initial QC

• SOP: Metagenome 2 - Taxonomic annotation

• SOP: Metagenome 3 - Functional annotation with MMSeqs 2

• SOP: Metagenome 4 - Functional annotation with custom HMM

• SOP: Metagenome 5 - Functional annotation with CARD RGI

• SOP: Metagenome 6 - Linking taxonomy and function

• SOP: Metagenome 7 - Assembly and binning

• SOP: Metagenome 8 - Multi-tier profiles

• SOP: Toy/tutorial data

• Tutorials

• Tutorials: 2026 - introduction to the command line

• Tutorials: 2026 - server setup

• Tutorials: 2026 CBW 1 - marker gene profiling

• Tutorials: 2026 CBW 2 - alpha diversity, beta diversity, and differential abundance

• Tutorials: 2026 CBW 3 - metagenomics and read-based profiling

• Tutorials: 2026 CBW 4 - metagenomic assembly and binning

• Tutorials: 2026 CBW 5 - assigning functions to metagenomic data

• Tutorials: 2026 CBW 6 - visualisation and finding functional significance