Ion Torrent data quality impressions?

[rcorbett]

Hi.
We have an Ion Torrent PGM where we have sequenced a number of genomes. Looking at the TMAP alignments we definitely see sequencing errors of the indel variety around homopolymer regions in the reference. The homopolymer runs don't necessarily have to be more than two consective bases either.

Some quick analysis showed me that the positions of the indels in the reads aren't completely random, and do stack up in the alignments, which could cause false positives in the indel calling (as well as potentially interfering with true variants that are in the region).

Downloading example E. Coli data from the Life website I see the same sorts of errors.

To my dismay when I google this I find all sorts of technical and sponsored reports from Illumina et al, pointing out the errors in Ion Torrent data. Furthermore, I see the reports getting fired back from Life discounting all the analysis in the first paper, and so it continues.

My question:
Can anyone who has sequenced and analyzed data on the PGM objectively comment on the rate of indels in the reads? I would like to hear if other people have seen what I've seen, or even better if they know of a magic fix.

thanks!