Bracken needs reference data. GA has the data manager but I wasn't sure what kraken2 DBS to convert, then I forgot about this. In the short term, we also need to consider how much space dbs will take up compared to what is available in /mnt/custom-indices.

OK, worth waiting til the move to ETCA is done?

The pre-built databases of kraken2 and bracken are available on https://ccb.jhu.edu/software/bracken/ and the DBs size is listed here https://benlangmead.github.io/aws-indexes/k2 . Hopefully, it can give us some ideas how much diskspace is required.

Note:
This GTN material uses PlusPF https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/taxonomic-profiling/tutorial.html#k-mer-based-taxonomic-assignment-with-kraken2

So we probably just want to download PlusPF and standard (see the index link above) for now.

from Valentine:
I chatted with Mike before, the answer was I tried previously what was available but quite old db from 2021. We agreed to use the 2023 ones
2:39

StandardRefeq archaea, bacteria, viral, plasmid, human1, UniVec_Core6/5/2023

2 ..PlusPFStandard plus Refeq protozoa & fungi6/5/2023

IM: can we get downsampled versions of the databases?

bracken is installed now