using multiple de novo assemblies to aid in exon joining

[jbio]

I have multiple de novo transcriptomes from related, but not necessarily inter-mappable species. For a given transfrag however, there appears to be some species that can assemble the full-length transcript, while others appear to have the same transcript assembled in pieces. A quick BLAST check of this confirms that I'm getting some partials and some full length transcripts for what are clearly orthologous sequences.

Does someone know a pipeline for this kind of application? I can imagine some kind of wrapper for BWA-mem, BLAST, or BLAT would do the trick, but thought I would consult the collective consciousness to see if anyone knew of an existing solution out there already.