Is there a way to filter on the Kalimari database?

To filter the Kalamari database, e.g. leaving out milk bacteria only to detect spoilers or contaminants, but the Kalimera list contains a lot more than that, you can:

  1. Look at a publication etc. to find a list of bacteria to remove.
  2. Change the regex ^.*Gallus|Homo|Bos.*$ to ^.*Gallus|Homo|Bos|Bacterium1|Bacterium2...|BacteriumN.*$

Milk pathogens are somewhat known, Salmonella, Escherichia… It might be easier to retain reads only mapping to pathogens instead

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