Sampling the suffix array with minimizers

Abstract

Sampling (evenly) the suffixes from the suffix array is an old idea trading the pattern search time for reduced index space. A few years ago Claude et al. showed an alphabet sampling scheme allowing for more efficient pattern searches compared to the sparse suffix array, for long enough patterns. A drawback of their approach is the requirement that sought patterns need to contain at least one character from the chosen subalphabet. In this work we propose an alternative suffix sampling approach with only a minimum pattern length as a requirement, which seems more convenient in practice. Experiments show that our algorithm achieves competitive time-space tradeoffs on most standard benchmark data. As a side result, we show that nʹ arbitrarily selected suffixes from a text of length n, where nʹ < n, over an integer alphabet, can be sorted in O(n) time using O(nʹ) words of space.