Hello, I am using the GalaxyEu server and working on analyzing some shotgun sequencing data from soil, produce, and manure amendment samples. I am using Kraken2 for the taxonomic classification. What reference databases should i choose in the tool parameters? Thanks for any help and guidance.
Hi @bgood07,
it depends on your goals. Personally, I suggest mini-kraken2 db: it has the same data (species) as equivalent full-sized db, but it is significantly smaller, so, you’ll get fast processing speed. Try it on a sample or two. If you are happy with the results, use it.
Kind regards,
Igor
Thank you. Will give this a try. Also, have you ever used galaxy to analyze antibiotic resistance gene abundance and diversity with shotgun metagenomic data? Do you have any suggestions on the workflow or tools that should used for this analysis? Such as AMRFinderPlus? Thanks.
Hello @bgood07
I’m glad the advice from @igor helped!
He may have more to add, but meanwhile I’m wondering if you have seen the 
Galaxy Training Network (GTN) tutorials? These are a great complimentary resource to publications, since most are based on an original paper and demonstrate how to translate command line analysis methods to those same (or similar!) tools as hosted inside of Galaxy.
You can search with keywords like this example:
- GTN Materials Search (query=antibiotic)
Or go to the top level and browse by Categories!
Or check to see if there is a Learning Pathway (exact, but also related domains!)
You’ll also find tutorials linked from the bottom of tool forms (when that specific tool is included in one). The Help section will also have some short advice – and this will cover any “Galaxy specific” advice, too.
For the tool you asked about, AMRFinderPlus, the usage guide is hosted at the original tool source at NBCI.
While tool forms will usually also have Help notes at the bottom, these tools will work about the same in Galaxy and we can help if you get stuck, just start up a new topic, share your history, then explain what is going wrong and the community will help to troubleshoot.
To help get you started, there are a few ways to use AMRFinderPlus.
- AMRFinderPlus NCBI Antimicrobial Resistance Gene Finder (see Guide link above)
- abriTAMR AMR gene detection with AMRFinderPlus
- Usage Guide and publication → abritamr/README.md at master · MDU-PHL/abritamr · GitHub
- staramr Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes
- Usage Guide and publication → staramr/README.md at development · phac-nml/staramr · GitHub
Then a newer tool suite (still in development, but you can use it at UseGalaxy.eu for now)
- MLST, AMRfinder, and STARamr Analysis Extracts MLST, AMRfinder Plus, and STARamr results from JSON input.
- See the Help on the form to learn about how this works plus related tools.
To find workflow templates you can try..
- Review the InterGalactic Workflow Commission’s (IWC) production quality workflows at → Workflow Details | Galaxy IWC
- Search with keyword “antibiotic” discovered the workflow amr_gene_detection-main). Visit to read about the details. You can import to review closer, then use it as is or make edits to customize.
- This site is a bit new and the example data function may not work well, but that is coming soon! Meanwhile, the GTN is a good resource for example data. Please let us know if you can’t find something suitable!
-
Search the Activity bar → Workflows → Public Workflows tab at any public Galaxy server. This will locate workflows shared by the community of users at that specific server, plus those published by the GTN and IWC. Later on, you can share your workflow too!
Go to the tab and type in your search terms. The workflow name, description and tags are all searched against.
Whew! That is a lot of information! But I want to add one final item .. if you are new to Galaxy, running through at least one of our Introduction tutorials will be very helpful to learn some basics about navigating the application. This is a nice short tutorial that will teach you how to use intermediate tools, how to create and edit a workflow, and how to share your data with collaborators.
I hope this helps! 
1 Like