nselem
commented
6 months ago I'm sorry for the delay, we hope your workshop was a success. We run kraken2 with the 2020 Standard Compatible database from benlangmead repository. We did not use the AWS machines to run kraken2, we upload precalculated results.
Greetings from The George Washington University!
We are preparing to do the workshop next week and I am going through the taxonomy notes. In Issue #68 you mention that we refer to the database vs minikraken, however it is not clear exactly what kraken database you are using in the analysis. I would like to replicate the exercise. Even if we don't include it in the workshop I would like to be more informed in discussing. Especially with the databases being hosted in AWS, this becomes in important step to document more fully.
Can you please refer me to what database you used. Once we have that, is it straightforward to refer to that in the "--db kraken-db" portion of the command given in the materials?
In our workshop we have the option of having larger VMs than the ones in the base Carpentries Workshop, though given time I doubt we'll do this step in the class. However, I will let our learners have access to the VMs for at least a week after the workshop so if they want to explore on their own I want to give them more complete information.