What pipelines are available? There are several computational pipelines that offer a user the computational power to analyze metagenomes on the cloud. We have explored KBase and will list several other pipelines. Now we will use Nephele to dig into a different dataset, focusing on data equity and quality control.
Upon successful completion of this module, you will be able to:
- MO 4.1. Describe the importance of processing reads before use.
- MO 4.2. Examine different approaches used for processing 16S reads.
- MO 4.3. Evaluate the output from a Nephele pipeline.
- MO 4.4. Justify your conclusions based on data.
- MO 4.5. Propose a future experiment based on your results.
- MO 4.6. Given a complex genomic DNA sample, the participant will be able to list the steps for creating an amplicon library (e.g., 16S), sequencing the sample, pre-processing the reads, and inferring taxonomic representation.
In Module 4, you will again have Top Hat Review Questions to exercise retrieval practice and reflect on the Module 4 video and Nephele exercise.
A JoVE Critical Thinking Scenario and Discussion Forum 2 will provide an opportunity to discuss soil samples and how to process them, sequence, and analyze the results.
Please, review the guidelines (opens in new window) for the data analysis project. Video Overview (opens in new window) We don’t want this capstone project to catch you by surprise as we near the half-way point of the course!
Your podcast script draft is due for peer reviews. Submit on Moodle and return to access your peer review assignment. You will have one week to conduct peer reviews of scripts and answer a series of questions about the writing.
We realize you have several assignments and appreciate your hard work and engagement with the materials and discussion forums.
To complete this module, you will need to:
- Watch Module 4 video and complete Top Hat questions.
- Complete Nephele activity after reviewing the dataset and article. Complete Top Hat questions on Nephele activity.
- Watch JoVE article/video and participate in the forum.
- Submit your podcast script for peer review. Begin peer review of a script
Please do not hesitate to reach out or ask a question on the Student Forum. Take care!
Things To Come by Broke For Free is licensed under an Attribution-NonCommercial-NoDerivatives (aka Music Sharing)