Welcome @prof.garrison.smc
This is a good question! Would you like to share some more details about the data source? I don’t see Kraken2 indexes but might be looking in the wrong place. I also don’t see a “download index” option, just the API connection for batches of data.
Then, I can share what we have already (most of the standard indexes). This just came up this morning! Popular tools! → Kraken2 databases question - #2 by jennaj
My initial thought is … would this group be interested in working with the Langmead lab, and would either be interested in generating new indexes for the wider Kraken/2 user community based on the new data stream? Then, questions like is this even possible or is it another curation project? If possible and resourced, then this index would have reproducible, open source data hosting, and could flow down to everyone, including Galaxy. But, I might be missing something about this that doesn’t make sense, so I would be curious what you think more!
Two more options that would only need a fasta version of the index is BLAST and VSearch. They seem to have these already indexed, so maybe write to them and ask? Any fasta from the history can work with the Galaxy versions of these. If there was other metadata in mapping files, either cvs or tsv could be used with data manipulation tools, too.
Let’s start there! Fewer silos is better for researchers, but sometimes the connections are complicated! 