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Independent Exploration: Comparing Individual vs Co-assembly Approaches

Overview

Now it’s your turn! You’ll use the same R analysis workflows to explore MAGs generated from co-assembly and compare them with the individual assembly results we examined together.

The Workshop material is available to download in Figshare

Your Task

Using the R Markdown documents from the previous sessions, analyze the co-assembly bins and compare the two approaches:

Link to R Markdown: Tiara and CheckM2 Exploration Link to R Markdown: dRep and GTDB-Tk Exploration

Key Questions to Answer

Work through the same analyses, but now comparing individual assembly vs co-assembly:

  1. Quality comparison - Which approach produced higher quality MAGs?

  2. Taxonomic diversity - Which approach recovered more families? More species?

  3. Contamination patterns - Does co-assembly have more contamination? Why?

  4. Representative MAGs - Which approach contributed more to the final dereplicated set?

  5. Target organisms - Which approach better recovered important coffee fermentation taxa (Lactobacillaceae, Acetobacteraceae)?

  6. Your recommendation - Based on your findings, which assembly strategy would you recommend for coffee fermentation studies?

Prepare to Share

Be ready to discuss:

  • Your recommendation (individual, co-assembly, or both)
  • Key evidence supporting your choice
  • One interesting finding from your comparison
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