I got a rather unusual question and would appreciate suggestions or discussion. Let say one has a good set of high quality sequencing reads, purportedly for bigfoot or sasquatch, which is likely a great ape, but no more is known than it is likely closer to Homo than to other great apes. But may be not. If a goal is to do some population genetics studies with this data set, one needs to assemble its genome and get as much variant calling as possible, and then run those comparisons. De novo assembly is not likely an option (is it?), so what are options for reference assembly? If using the human genome as a reference, there is a danger of loosing a lot of crucial variants and getting quite skewed results. If using the chimp or gorilla genomes for reference assembly, then how to proceed after that with variant calling and comparison with human variations? How would you approach this?