I am trying to improve the annotations in a region of the Sheep genome and have compiled at set of 60 Sanger sequenced ESTs from sheep which I would like to assemble with a set of 2,863,891 sheep Illumina reads from a transcriptomic study. These are the reads that mapped to a syntenic region in the cow genome (this being a much better assembly and well annotated). I want to combine these two different sets to obtain the best possible set of transcripts for this region of the sheep genome. I've looked at Trinity but have not seen an option for incorporating ESTs.
I would be grateful for any suggestions.