I have RNASeq of algal cultures so my samples are not really axenic. Instead, the presence of some bacteria or fungus is to be expected. I assembled my reads with Trinity and now I would like to estimate the origin of each individual contig. Ideally, I would like to get visualization of where the contamination is coming from on the Tree of Life as a:
- quality metrics that the origin of my contamination makes sense (and I see what I expect to see for algal cultures)
- to remove contaminants and "clean" the assembly
Is there any tool that could do this for me?
I started by automatically outputting the "best" blast hit for each contig, but I am getting large variety of the hits and I am not sure how to summarize them or properly assign them phylogenetically.
Thanks for help.