Fingerprint computation on b-length substrings. When looking for overlaps between S and r, the fingerprints are computed on the substrings r[x, . . ., x+b -1] and S[y, . . ., y + b - 1], respectively, where x and b are set before the contig's extension phase. We require an (almost) exact b-length match between r and S in order to include r in the set of putative overlapping reads, by setting fH (r[x, . . ., x + b - 1]) = fH (S[y, . . ., y + b -1]). Using such a method, the suffix-prefix overlaps that can be detected are those of length l ≥ x + b.
Nadalin et al. BMC Bioinformatics 2012 13(Suppl 14):S8 doi:10.1186/1471-2105-13-S14-S8