Good morning team!
We hope you enjoyed the weekend and are ready for a new module in the course. Module 2 will dive into metagenomics and attempting to assemble metagenomic sequences into genomes. For this, we will use the KBase platform, and Dr. Jason Whitham is a fantastic resource and true expert. He created the ‘silver narrative’ we will use. Create a free KBase account.
Our Unit 2 checklist can be found here.
Group 1 will write a summary of the first article we annotated that features some of the techniques we will be using.
In the lab this week, we will complete the library cleanup and quantify each sample before pooling all samples into one tube for sequencing.
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Overview
What are MAGs? You will learn some foundational methods for processing metagenomic data and how to interpret common analyses of this type of data.
Upon successful completion of this module, you will be able to:
- MO 2.1. Perform quality control of read libraries.
- MO 2.2. Predict taxonomic population structure of environmental shotgun reads.
- MO 2.3. Identify high-quality bins to extract and annotate.
- MO 2.4. Annotate genes of extracted MAGs.
- MO 2.5. Place MAGs into a species tree.
- MO 2.6. Build metabolic models.
To complete this module, you will need to:
- Watch Module 2 videos
- Create an account with KBase
- Complete the TopHat questions for this module.
- Participate in the discussion forum
- Share resources you created in the class notes.