Module 4: What pipelines are available?

Hello!

We hope you enjoyed the weekend and are ready for a new module in the course.

Module 4 will ask: 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.

Our Unit 4 checklist can be found here.

Checklist icon in gray box. Purchased from The Noun Project.

Article 2 was complex. I encourage everyone to review the annotations. Groups in charge of the summary should share a GoogleDoc with me by the end of the week.

This week we will open up the lab tomorrow for you to join if you want and complete the Nephele activity posted on Moodle. You are not required to come to Jordan Hall, though it will be a place for you to work. You can work on the Nephele assignment on your own in another place or come in and talk to peers. I will also release updates to LabArchives so that you can work on Nephele analyses of OUR 16S marten datasets. First, complete the Moodle Nephele assignment. 

Podcast scripts are due for scholar peer review this week. This is your chance to learn from others and proofread!

Finally, we want you to review the guidelines for the final data analysis project.

CG

Overview

What is diversity? In this module, will define alpha and beta diversity and explore why researchers use diversity metrics to describe microbial communities.

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.

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.
• Review the guidelines for the final data analysis project.
• Submit your podcast script for student scholar review. Begin student scholar review.