I have several contigs (~1 kb - 20 kb) from a metagenomic sample which, according to marker gene analysis, belong primarily to one eukaryote or several prokaryotes both bacterial and archaeal. All of the contigs have a very similar GC content.
What is the best way to separate the eukaryote DNA from the prokaryote without using references (eg, blasting each contig to a reference won't work, most of the contigs are too far removed from any reference)? Codon biases? Looking for certain genomic features?