Ultimately, is there anything you could do with repetitive regions? Like, were the problems with the heuristics or just a mismatch between ~100 base reads and multi-kb repeats?
most people have moved to techniques that produce longer reads with higher error rates. good coverage + longer reads overcomes the higher error rate. You can read the DALIGN paper by Myers to learn more. Or read https://dazzlerblog.wordpress.com/author/thegenemyers/
