use BLAT to ASSESS an ASSEMBLY - this program parses the output of a BLAT run of transcriptome vs. a genome. It returns 1) Total % coverage, 2) Average number of contigs mapped per mapped transcript, and 3) number of potential rearrangements. It will also create a file with transcript IDs that occur at regions that are potentially misassembled. It is simple to run. Just run the blat (transcripts vs. genome) and then run the script with the blat-output and your transcript-fasta-file as arguments.