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.
Dr. Jason Whitham will introduce a the “Silver” case study using a KBase narrative on Metagenome Assembled Genomes (MAGs). With this activity, you will perform quality control of read libraries, taxonomic classification, assembly, binning, and annotation, culminating in the creation of metabolic models. In the second case study, “Gold: Where is Delftia?” you will reproduce a similar workflow but using a dataset, you identify to search for a unique genome.
To prepare you for these KBase cases, we have created short videos. To reinforce your knowledge, we have a series of Top Hat questions focusing on the process, findings, and limitations of these approaches.
Finally, we have our first JoVE Critical Thinking Scenario and Discussion Forum 1. The article we will analyze is entitled: Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples. J. Vis. Exp. (94), e52117, DOI:10.3791/52117 (2014). It will introduce another level of complexity in biological samples and serve as a prompt for our discussion forum.
At this point, you should identify a couple of topics for your podcast assignment and schedule a time to discuss logistics with Jason Evans Groth.
We look forward to productive discussions and analyses!
Things To Come by Broke For Free is licensed under an Attribution-NonCommercial-NoDerivatives (aka Music Sharing)