Decontam by group necessary?

[sachasuca]

Is it necessary that I run decontam separately for different sample types when they all are low-biomass? I have ~300 swab samples from multiple body sites and breast pump equipment (e.g., bottles and tubing). All of the sites are expected to be low-biomass, they were all extracted together and run on the same Illumina sequencing run. I have 13 negative controls and I have run decontam using prevalence-based filtering. I realize there may be an advantage in conducting decontam separately by group type if sample types differ significantly in the amount of endogenous DNA each contains; however, I'm not sure whether you recommend doing it in this case.

[benjjneb]

If you are using prevalence-based filtering on one technical batch (as you've described) then there is no need to separate by sample type, you can and probably should just group them all together.

Separating samples of different types is more important for avoiding possible false-positives with the frequency method. Given that all your types are low biomass and from a common technical batch, it seems like it would be OK to group them all together for the frequency method as well, but I don't have enough experience with that scenario yet to give you educated practical guidance. I might try both ways.

[sachasuca]

Thanks for the feedback!