Teaching school children eDNA bioinformatics (sequence files to Krona chart) in 30 minutes

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I have prepared an online teach-the-schoolteacher eDNA demo. The teacher is guided to build and run the following eDNA bioinformatics work flow from scratch in 30min. The teacher is then able to teach his/her school students in 30 mins in a classroom setting.

DATA LOADING

  1. load reference database

  2. load forward and reverse Illumina eDNA sequence files

  3. combine sequence files in a collection of paired reads

SEQUENCE PROCESSING AND QC (FASTP)

  1. Adapter removal, trim, Phred quality filter and paired read merge (and review QC plots)

TAXONOMIC IDs (VSEARCH)

  1. Run VSEARCH to get taxonomic IDs.

PRODUCE KRONA PLOT OF DIVERSITY

  1. Reformat Vsearch output tab file for Krona Plot

  2. Produce Krona Plot

Reach out to me if you are interested to know more.

Adam

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This is a great outreach idea, going from raw Illumina reads to a Krona chart in 30 minutes is a real hook for kids since the interactive plot pays off visually. One thought: the tight timing lives or dies on data size, so pre-subsampled read files keep VSEARCH fast website enough to stay in the window. Might also help to have the workflow pre-shared as a Galaxy import so teachers aren’t rebuilding step by step if the clock runs short. Nice work Adam.

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Thanks Vikior. My demo project has just one sample so runs very quickly. I also have a 3 sample version to show how to parallel process multiple samples. I can also create a full (16 sample) version. I am not sure how to share it all fully.

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Is there anyone else planning to teach kids this kind of thing. I plan to offer to teach teachers rather than teach kids.

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Hi @Adam_Hillier

If you want, this would be a nice addition to the GTN.

And we have more teacher resources here, and these are dynamic and can grow too! The TIaaS resources would be critical for an instructor hosting a live workshop.

Nice work and hope this helps! :slight_smile: