The SMRT sequencing technology developed by Pacific Biosciences (or PacBio) is gaining popularity due to its ability to sequence individual molecules in real time and the very long reads it produces (10-50X longer than those from Illumina). But for those who have experienced it, analyzing PacBio data isn't as straight-forward as it had appeared. The root cause of the difficulty is its high error rates - up to 15% at the subread level. Assuming subreads are independent, simple calculation shows that requiring 4 full passes would produce Reads of Insert (ROIs) with error rates of 0.05%. The error rates we actually observe, however, are nearly two orders of magnitude higher. This suggests that the subreads are not acutally independent. What it also means that PacBio data analysis is tricky: one should always keep error rates and error profiles in mind when evaluating the data. It will always take some tuning and head-scratching to develop the "optimal" analysis strategy for any bioinformatics project involving PacBio data.
If you are frustrated with your PacBio data analysis project, talk to us. Our Lead Bioinformaticians have 150 years combined experience in bioinformatics research and development, many have served as professors in major U.S. institutions, and some of them are among the very few that are uniquely experienced in handling PacBio data.
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