use RNA transcripts to assess assembly - this program parses the output of a BLAT run of transcriptome vs. a genome. It returns 1) Total % mapped, 2) average %coverage of a mapping, and  3) number of transcripts mapping to a single contig/scaffold. 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.