I ran kraken on the same file twice- once on the galaxy server using the "bacteria" database, and once using my local installation using the "standard" database.

The galaxy results were as follows: https://postimg.cc/YhRMVWx5

The local kraken results were as follows: https://postimg.cc/gXzf3MCr

What do I need to do to get my local kraken results in line with the one on Galaxy? To clarify, how do I alter my kraken call (on my system) to give me the results I see on Galaxy?

Hello,

The Kraken databases that Galaxy includes are available from the source. If you create/install Bacterial in your local, the results will be similar to those at Galaxy Main https://usegalaxy.org.

Kraken Data Manager: https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_build_kraken_database/6d7aef331be9

More about the databases: http://ccb.jhu.edu/software/kraken/MANUAL.html#custom-databases

Thanks! Jen, Galaxy team