Incubator Lesson Spotlight: Bash and R for Metagenomics

Highlighting this lesson from The Carpentries Incubator, Bash and R for Metagenomics.

The Incubator Lesson Spotlight highlights a lesson under development by our community in The Carpentries Incubator. In this edition, we look at the progress being made on the Metagenomics lesson, and hear from the authors about how The Carpentries community can get involved with the ongoing development of this lesson.

Lesson Profile

  • Title: Metagenomics
  • Lesson Pages: https://carpentries-incubator.github.io/metagenomics/
  • Lesson Repository: https://github.com/carpentries-incubator/metagenomics

Learning Objectives

  • Acknowledge the importance of well-organized bioinformatics projects and apply this sense of tidiness to metagenomics data.
  • Learn and implement the guidelines for reproducible metagenomics projects.
  • Understand and apply the basics for Bash and R programming languages.
  • Use of Bash and R programming languages to assess and manipulate metagenomics data.
  • Learn and use the steps and tools for a complete analysis of shotgun and 16S metagenomics data.

Target Audience

Genomics and metagenomics enthusiasts; newcomers to the bioinformatics world; biological science undergraduate, postgraduate students and researchers. We do not assume previous knowledge of Bash, R or metagenomics for the lesson.

Lesson Progress

Our lesson is in the alpha stage. All episodes are completely written in the sense that they are at minimum a viable product ready to provide the learners their teaching goal. Nevertheless, as with any carpentries lesson, we seek continuous improvement. Specifically, now we are discussing how to avoid some pre-calculated data, how to include a 16S section, and if we should include other metagenomic tools for quality check. We have already taught it twice only by our team members. But we are looking forward to new opportunities to share it. The instructor notes are ready and we are eager to collaborate with interested instructors.

We developed three sections aiming for a full metagenomic workshop divided into three sections: organization (https://nselem.github.io/organization-metagenomics/), shell-metagenomics (https://nselem.github.io/shell-metagenomics/) and metagenomic diversity analysis (https://carpentries-incubator.github.io/metagenomics). The first two were adapted from the Data Carpentries Genomics curriculum to this metagenomics lesson; their goal is to introduce learners to what to think about before starting a metagenomic project and to basic Linux terminal skills. The third section uses the terminal to explore the quality of our metagenomics data and leads into an introduction to the R language to manage metagenomics data and compute frequently used metrics.

How You Can Help Develop This Lesson

To take our lesson to beta status, we would love to bring instructors from the Carpentries community to teach this lesson in their city and to contribute to its development. Also, we welcome feedback related to the contents and the user-friendly tools for metagenomics as well as direct contributions to solving already identified Issues (https://github.com/carpentries-incubator/metagenomics/issues).

Please contact us to collaborate:


About This Series

Incubator Lesson Spotlight is a regular feature in The Carpentries blog and Carpentries Clippings newsletter, highlighting the great work our community is doing to develop new lessons in The Carpentries Incubator. Developers of any lesson in the Incubator are encouraged to submit details about their material for inclusion in the series. If you would like to increase the visibility of your lesson and encourage Carpentries community members to contribute to its ongoing development, fill in this short form.

Dialogue & Discussion

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