I know that there are several approaches to detect contamination in submitted NCBI transcriptome studies databases, but since I am doing a literature review, I would appreciate if you add up to my list with your suggestions.
Do you mean vector sequences?, you can use the NCBI Univec database sequences and match with the RNA-Seq data to eliminate any contaminating sequences. Follow this link for more information:
VECSCREEN only screens the vector sequences not removes them so you have to write a script to remove it (I used it personally). You can use SeqClean tool it will remove all the vectors then input its .cln and .qual file into "cln2qual". I think it will work for you. :)