khyox
commented
2 years ago Hi @rjsorr,
You have details about the robust contamination removal in the paper, and more details in:
- The supplementary material appendix S4: Recentrifuge manual, or
- The Recentrifuge wiki in Understanding the messages of the robust contamination removal algorithm
If you want to customize the algorithm, you are more than welcome to fork the repository and change the code as you wish to tailor it to your specific needs, only abiding by the terms of the license. If you think that your modifications to the code may be of general interest to the community, I would be happy to review and add your contributions to the main branch. Thanks.
Hi, is it possible to get some guidelines for the robust contamination removal? At what level should taxa be removed and where should this be considered? For example "Critical" should be removed but what about taxa identified as "severe" or "mild", where does the line go? or would you define a cut-off using the score value in the excel file? Also, for the html output what is actually being removed from the final plot and at which level? and is it possible to control this as a user, lets say I want to keep "mild" in the final plot?
I ask, as with default settings I am getting 40 taxa identified as "severe" contaminats.
regards