This step is required to remove reads corresponding to rRNA from Helicos CAGE datasets.
Since the error rate of Helicos is high and includes many insertion / deletion errors, the only viable option was to match sequences against rRNA sequences (U13369.1) using a non-heuristic alignment algorithm. Due to the amount of data a SSE parallelized version of Myers bit-parallel algorithm was implemented.
All reads matching the reference rRNA sequences with up to 2 errors are discarded at this step. Software available at fantom.gsc.riken.jp/5/suppl/rRNAdust/