Microbiome analysis using NGS technology
Description:
This activity is to introduce students to analyzing microbiomes using next generation sequencing technologies and bioinformatic analysis. Students will be introduced to next generation sequencing technologies, their uses and drawbacks for microbiome analysis and the biological questions you can answer using these techniques. Students will get hands on experience analyzing a real dataset, generating publication quality figures and interpreting the results.
The module will follow the STREAM model with before-class, in-class and out-of-class activities.
Intended Learning Outcomes:
- Understand the terminology for describing ecological communities
- Explain the different sequencing technologies/'omics' and their uses
- Interpret biological meaning from sequencing data
- Understand and explain graphical interpretations of microbiome analysis
| Resources | Tasks | Supports | |||
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Before-class activities |
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Scientific papers |
Read the set text and answer questions about text onto the forum ↓ |
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Brightspace |
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Instruction material and links to software for download |
Read through the software instructions and install the required software onto their computers ↓ |
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Teacher |
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Mentimeter |
Answer a short quiz on microbial analysis using next generation sequencing technologies ↓ |
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None |
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Explain everything video on NGS sequencing technologies and sample preparation |
Watch some introduction videos on next gen sequencing technologies and sample preparation ↓ |
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Brightspace |
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In-class activities |
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PowerPoint presentation and video |
Students listen to short lecture ↓ |
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Teacher and guest lecturer |
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Tutorial available on Brightspace. Links to tutorials of popular bioinformatic pipeline software. Bioinformatic software (qiime and R) |
Student perform bioinformatic analysis on a real dataset ↓ |
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Teacher and assistants |
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Mentimeter |
short quiz to promote discussion of results ↓ |
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Teacher |
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Out-of-class activities |
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Brightspace and bioinformatic software (qiime and R) |
Prepare a report and submit to brighspace |
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Peer review and teacher |
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Additional information
This class is given on one day of a two week summer school. The students will attend 1-2 lectures from a guest lecturer before this class. This class will take 5-6 hours during the residential course with additional tasks before and after the class. The in-class activities will be performed in 2-3 cycles of short lecture, tutorial and then discuss results with quiz.