I am studying de novo (non-model) genome annotation and would like to use a well characterised organism to test some of my methods. To this end I am looking for an assembled de novo transcriptome dataset for Drosophila melanogaster, preferably assembled from short read data. Does anyone know where to find such a dataset? Thank you!
In this paper, you can find a list of SRA accessions for Drosophila short reads. They have also provided the statisitcs for different de-novo assemblers: Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. Unfortunately, they do not seem to provide the assembled transcripts. I imagine that for D. melanogaster it is probably rare that researchers would be doing de-novo transcript assembly as there is a very good genome to assemble to.