I'm currently working with a eukaryotic genome (~1Gbp) from a small organism which is very difficult to extract quality DNA from. We've performed some preliminary sequencing on DNA pooled from multiple individuals.
Does anyone have any experience working with this sort of read data? Are there any methods or assemblers which are more suitable for dealing with data with this sort of very high polymorphism? Are there any tools which can pre-process the reads to reduce the level of polymorphism to something more approximating a diploid genome?
I'd appreciate any advice or experience from the community.