Microbiome research typically involves the study of the collective genetic material of microorganisms from a wide variety of natural environments. As a result of the efforts carried out by scientists across this diverse and expanding research field, over 1.9 million raw read microbiome datasets have been collected and made publicly available.

Detailed analysis of collected data is increasingly redefining our understanding of microbiology by providing unique insights into microbial community composition, the processes performed by the microbes and their relationships with their surroundings and each other.

MGnify (Mitchell AL, et al., 2020) is a platform that provides free assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. The resource accepts user-submitted data and provides standardized pipelines that offer taxonomic and functional analysis of microbiome datasets.

Inside of the Workshop

In this two day remote tutorial, you will explore common approaches to analysing and annotating contigs produced from a metagenomics assembly. The course will be a mixture of introductory lectures, followed by hands-on practicals. Due to time constraints, you will either investigate pre-calculated examples or use a web browser to explore outputs via the MGnify website (www.ebi.ac.uk/metagenomics). By the end of the course, you should understand how to process contigs, functionally and taxonomically characterise the contigs, and be able to generate metagenome assembled genomes from your assemblies.

Syllabus

Part 1 – Next steps after metagenomic assembly

· Introduction (lecture) 

o What constitutes a good assembly?

o How we estimate assembly quality

o Host decontamination

o Submitting to ENA

§ Raw read deposition vs assembly

· Hands-on – Assessing quality and decontaminating host DNA in assemblies

Prerequisites – Installed bandage, and ability to install docker container. 

Part 2 – Annotating bacterial contigs

· Overview of MGnify annotation pipeline

o Getting assembly data into MGnify

o Taxonomic assignment

o Functional characterisation

o Pathways/systems

· Hands-on – Accessing annotations via MGnify website

Prerequisites – Up to date web browser, e.g. Chrome. Ability to install docker containers. 

Part 3 – Annotating viral contigs

· Viral contig annotation using the VIRify pipeline

o VirSorter/VirFinder

o ViPhoG HMMs for taxonomic assignment

o Other tools/issues

· Hands-on – Look at annotation outputs, on the command line and in MGnify website

Prerequisites – Up to date web browser, e.g. Chrome. Ability to install docker containers. 

Part 4 – Metagenome assembled genomes (MAGs)

· Generation of metagenome assembled genomes (MAGs) from assemblies 

o How to generate MAGs

o Assessment of quality (MIGMAGs)

o Taxonomic assignment

o Dereplication of MAGs across samples

· Hands-on Generating MAGs and Assessing Genome Quality

o Go through the process of MAG generation and taxonomic assignment

Prerequisites – Up to date web browser, e.g. Chrome. Ability to install docker containers.

References

Mitchell AL, et al., MGnify: the microbiome analysis resource in 2020. Nucleic Acids Res. 2020 Jan 8;48(D1):D570-D578. doi: 10.1093/nar/gkz1035.