Abstract
Motivation Representing a set of k-mers — strings of length k — in small space under fast lookup queries is a fundamental requirement for several applications in Bioinformatics. A data structure based on sparse and skew hashing (SSHash) was recently proposed for this purpose [Pibiri, 2022]: it combines good space effectiveness with fast lookup and streaming queries. It is also order-preserving, i.e., consecutive k-mers (sharing a prefix-suffix overlap of length k–1) are assigned consecutive hash codes which helps compressing satellite data typically associated with k-mers, like abundances and color sets in colored De Bruijn graphs.
Results We study the problem of accelerating queries under the sparse and skew hashing indexing paradigm, without compromising its space effectiveness. We propose a refined data structure with less complex lookups and fewer cache misses. We give a simpler and faster algorithm for streaming lookup queries. Compared to indexes with similar capabilities and based on the Burrows-Wheeler transform, like SBWT and FMSI, SSHash is significantly faster to build and query. SSHash is competitive in space with the fast (and default) modality of SBWT when both k-mer strands are indexed. While larger than FMSI, it is also more than one order of magnitude faster to query.
Contact giulioermanno.pibiri{at}unive.it, rob{at}cs.umd.edu.
Competing Interest Statement
R.P. is a co-founder of Ocean Genomics Inc.