Smooth $q$-Gram, and Its Applications to Detection of Overlaps among Long, Error-Prone Sequencing Reads

We propose smooth $q$-gram, the first variant of $q$-gram that captures $q$-gram pair within a small edit distance. We apply smooth $q$-gram to the problem of detecting overlapping pairs of error-prone reads produced by single molecule real time sequencing (SMRT), which is the first and most critical step of the de novo fragment assembly of SMRT reads. We have implemented and tested our algorithm on a set of real world benchmarks. Our empirical results demonstrated the significant superiority of our algorithm over the existing $q$-gram based algorithms in accuracy.