I have paired read HiSeq transcriptome data, and I've used a reference sequence to assemble it to a specific gene I'm interested in, but I'd like to sort out the phase of the reads to construct individual alleles from the assembly. I can do it by hand, using shared variants, but the gene is 13Kb and sorting out that many reads by hand is extremely time consuming and tedious. I don't have population level sampling, so statistical reconstruction using something like PHASE isn't feasible, nor do I have a set of known alleles to compare it to (this species hasn't been sequenced before).

Anyone have any suggestions?