i am working on a rna seq dataset which was sequenced PE with 454 and Hiseq. I have assembled 454 with newbler and hiseq using trinity. There is no reference available for the animal which i am working. So i wanted to construct a reference transcriptome using this information. We have lot of coverage more than 30X atleast. What is the best way to use this information to construct reference trascriptome ?
so far with my searching MIRA performs this hybrid assembly but it takes reads and do the assembly. I have the assembled transcripts and i need a pipeline of things i can do to use already assembled transcripts from illumina and 454 and built the reference.