15. What Should I Do Now?

Congratulations on completing this introductory course on metagenomics analysis! You’ve acquired foundational knowledge and practical skills in key areas such as interacting with the command line, Conda environments, read and assembly based appraoches, taxonomic classification, and antimicrobial resistance gene detection.

What you learn next is completely up to you but I would suggest analysing your own dataset, if available, as this will lead you to your own personal research questions whilst reinforcing the solid foundation that you have formed through this course. There’s many avenues of metagenomic analysis that we didn’t cover here, which will have varying degrees of applicablity depending on your aims. These include:

• Comparative metagenomics - Comparing metagenomic datasets from different environments or time points can reveal insights into how microbial communities change in response to environmental factors, such as pollution, climate change, or human activities.
• Strain-level analysis - Metagenomics can be used to study microbial populations at the strain level, revealing insights into the diversity and dynamics of closely related organisms. This information is crucial for understanding the functional roles and interactions of specific microbes within their environment.
• Functional profiling - In additon to detecting the presence of AMR genes, functional profiling of other molecular functions and metabolic pathways are often of interest to researchers.
• Virus identification - viral sequences are often abundant in metagenomic data and they can be identified, assembled, and analysed using specialised tools. The most abundant viral sequences typically belong to bacteriophages, but eukaryotic viruses are not uncommon.

If you’re really not sure what to focus on, my recommendation would be: find a metagenomics research paper that interests you, download their dataset (or a subset if theres too much data), and try and analyse the data using the methods described in the article and see if you get the same results. Good luck with your metagenomics and bioinformatics journey! Please contact me if you have any burning questions about this course or about bioinformatics in general.