16S Metagenomics Workshop based on Data Carpentry: successes and challenges

Authors: Bianca Peterson BLOG

We ran a 16S metagenomics workshop based on Data Carpentry materials at the North-West University, South Africa, from 24-27 October. A combination of lessons from Data Carpentry, as well as specific workflows for 16S data analysis, were used. We modified most of the lessons according to our main (critical) lesson’s dataset that we were using for 16S analysis. The following topics were covered: spreadsheet organization, shell, 16S analyses on HPC (using Shi7, NINJA and QIIME), R genomics and specific plots of 16S data in R. We extended the workshop to three full days to fit in all the lessons and decided on an additional half-day where attendees would have the opportunity to work on their own data. Twenty-three participants attended the whole workshop.

Group_photo

Here is a breakdown of the lessons, with successes and challenges mentioned for each:

Conclusion

The modified lessons (around the single example dataset) seemed to work much better. The cognitive load was greatly reduced, and they could really get to know the data since they were working on it from the first day. Participants didn’t mind an extended workshop - they actually appreciated it. After the workshop, several participants used what they learned during the workshop, and analysed their own data.

Word of thanks

We would like to thank Boeta Pretorius (NWU IT Director), Adelle Lotter (Acting director: NWU Academic and Office Solutions) and Professor Carlos Bezuidenhout (Microbiology department) for their support and for sponsoring the workshop. We would also like to thank the NWU IT team, Riaan Stavast, Thabo Molambo, Hannes Kriel, Martin Dreyer, and especially Ciellie Jansen van Vuuren, for going the extra mile to ensure all software were loaded and working on the HPC and for providing additional support in terms of internet access throughout the workshop.

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