Sampling the suffix array with minimizers

TL;DR

This paper introduces a new suffix array sampling method using minimizers that requires only a minimum pattern length, offering a practical and efficient alternative to previous alphabet sampling schemes.

Contribution

It proposes a suffix sampling approach based on minimizers that relaxes pattern constraints, improving practicality and maintaining competitive efficiency.

Findings

Achieves competitive time-space tradeoffs on benchmark data

Requires only a minimum pattern length, not specific characters

Outperforms previous alphabet sampling schemes in flexibility

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.