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@Minamehr Minamehr commented Oct 7, 2025

Add new tutorial: Host removal in metagenomic data (Microbiome topic)

This pull request adds a new tutorial under the Microbiome topic titled “Removing host contamination from metagenomic data.”
The tutorial guides users through:

  1. Mapping raw reads to a host genome using Bowtie2
  2. Extracting unmapped reads (non-host sequences)
  3. Re-running the same workflow for human contamination removal
  4. Generating clean reads for downstream metagenomic analyses

To Be Completed:

  • Input datasets (toy data) still need to be uploaded possibly to Zenodo and linked in tuterial.
  •  The solution boxes for certain hands-on steps may need adjustments once the new dataset is finalized.

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@Minamehr tuning in from the Australia node of the FAIRyMAGs hackathon.

I rendered this locally and looks good to me!

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🚫 [GTN Lint] <GTN:027> reported by reviewdog 🐶
This workflow is missing a test, which is now mandatory. Please see the FAQ on how to add tests to your workflows.

@bgruening
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@vinisalazar please add yourself as reviewer.

The liniting still needs to be fixed before we can merge.

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3 participants