How to run a metagenomic workflow from an ONT data, and do a downstream taxonomic analysis using kraken, krona and Pavian
Dear @bernt-matthias i am please struggling to create a working workflow from an ONT sequenced data, and doing a downstream taxonomic analysis using kraken, krona and Pavian, all to be included in the workflow. Can you please assist me with how to go about this project, all the tutorial videos i have watched only managed to get me as far as successfully uploading my data to my history and then naming it. I am struggling to come up with the right tool and parameters to set for each stage of the analysis. Thank you for your support
Welcome @Sonshine24
Let’s combine your other question into here.
We have tutorials here that cover examples of this analysis
Starting here seems like a good idea
Or, you can go directly to a tutorial like this one to learn how to adopt the tool usage when working with ONT reads
Then continue from the common starting point to work with the results later in a tool like Pavian
If you are brand new to Galaxy, following the Learning Pathway above will be well worth your time. It can be really frustrating to discover that “something went wrong” with an early analysis choice that didn’t show up until a later data reduction step. Maybe some QC step was missed or maybe a different reference data choice would have been better. Both of the tutorials I highlighted are included in the Learning Pathway and combined those should get you a solid understanding of how these analysis are done (anywhere) then how to navigate those choices in Galaxy.
Most of these tutorials were adopted from a publication that didn’t use Galaxy (instead, the underlying tool or a similar tool), and one specific tutorial might not have everything that you want to do. Many tools in Galaxy are not included in a Galaxy tutorial at all, but will have the original author tutorials, use guides, and related publications. Find a short overview of the resources we know about at the bottom of each tool form but supplement with your own publication methods that you want to follow.
Hope this helps! 
Thank you @jennaj for your support, I will go through the videos again and if I still can’t complete my analysis or encounter any errors can I please reach out to you again?
Thank you.
Yes, you can always ask questions about tutorials here, plus get help with troubleshooting errors. See the banner and pinned topics here for where to review problems and how to share your work for feedback. Include screenshots as needed but share links provide the most context.
You might also find an solution in some of the prior Q&A. Searching with the tool name or unique parts of the error messages can find related topics. Using the wizard on the bug report form is newer and worth a try too.
But anytime you are stuck, please start up a new topic, share the details, and ask about it.