I have been using newbler for a while now, and the rate of misalignments is very high. I have found that these are correlated with the homopolymer problem, but should be aligned correctly.
For example, this is produced in the 454PairAlign.txt (top is read, bottom is reference):
I have omitted the full reads for brevity.
The read has undercalled the two homopolymers. However, the best alignment suggested is clearly wrong since the GTA in the middle should be aligned, with two homopolymer gaps.
Has anyone found a way of getting newbler to correctly align such cases (eg different parameters)?
It seems like this must be a problem with the aligner, which appears to prefer three gaps plus two substitutions to two gaps (in homopolymers).