Best tool for cross plate contamination removal

Question

[godwin]

I want to perform a cross plate contamination removal before WTAs so I need recommendations for the best tool I can use. The transcriptomes are from microbial eukaryotes.

[GenoMax]

What is the contamination from? What is the significance of "cross plate" reference?

bbsplit.sh from BBMap suite allows binning of reads to multiple genomes at the same time. That would work best if you have the genome of interest available so you can do positive selection.