Week 5: Metagenomics

Week beginning November 25 2024

Topics

1. Metagenome profiling
2. Metagenome assembly and binning
3. Quality checks on MAGs
4. Taxonomic classification of MAGs
5. Functional analysis of metagenomes and MAGs

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Dataset and learning strategy

This set of tutorials uses some faecal metagenome samples from a paper from Mark Pallen’s group on critically ill patients on the Intensive Care Unit (ICU). They found that ICU patients had significant alterations in their faecal microbiome composition, including depletion of beneficial bacteria and an increase in potentially pathogenic species. This material is designed to be worked through by students engaged in as student-directed learning with peer-to-peer support but without face-to-face input from a facilitator. Although rooms have been booked as detailed below, students should as a group decide at the begining of the week how they wish to work–whether in one large group or several smaller groups, whether in the designated rooms or as hybrid event where some students work from home. Although sessions are designed to roghly fit within half days, students can decide how they wish to schedule the work. The final session requires no hands on work and so could be done via Teams.

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Room bookings

• Monday November 25: UG55C
• Tuesday November 26: UG55C
• Thursday November 28: Board Room
• Friday November 29: Board Room (but probably best done from home)

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Credits

This material has been prepared by Mark Pallen (mark.pallen@quadram.ac.uk)

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