Given that in a certain sequencing study, a big majority of the reads are not mapping to the origins of interest (human / mouse & yeast), I am looking for a tool / approach check for cross-species contaminations of the reads.
A quick BLAST of some sequences revealed some bacterial RNA, but I want to classify all of the reads. Can you recommend me a tool / approach / best practice to do this high-throughput.
I have found a few online, but as far as I can see most of them are made for bacterial metagenomic studies. Probably some of you experienced users have a quickhack or a best practice.
Thank you very much.