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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 theproblem of detecting overlapping pairs of error-prone reads produced by singlemolecule real time sequencing (SMRT), which is the first and most critical stepof the de novo fragment assembly of SMRT reads. We have implemented and testedour algorithm on a set of real world benchmarks. Our empirical resultsdemonstrated the significant superiority of our algorithm over the existing$q$-gram based algorithms in accuracy.

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