Is there a way to filter on the Kalimari database?

Authors: orcid logoEngy Nasr avatar Engy NasrAdd Contributions!

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

Persistent URL
Resource PURL: https://gxy.io/GTN:F00386
Still have questions?
Gitter Chat Support
Galaxy Help Forum