A Compressed Self-Index for Genomic Databases

TL;DR

This paper introduces a compressed self-index for genomic databases that leverages relative Lempel-Ziv compression to efficiently store, search, and access large collections of similar genomes.

Contribution

It extends RLZ compression by enabling fast search capabilities, creating an efficient self-index for large genomic datasets.

Findings

Achieves good compression ratios for genomic data

Supports fast random access to stored genomes

Enables efficient search within compressed genomic collections

Abstract

Advances in DNA sequencing technology will soon result in databases of thousands of genomes. Within a species, individuals' genomes are almost exact copies of each other; e.g., any two human genomes are 99.9% the same. Relative Lempel-Ziv (RLZ) compression takes advantage of this property: it stores the first genome uncompressed or as an FM-index, then compresses the other genomes with a variant of LZ77 that copies phrases only from the first genome. RLZ achieves good compression and supports fast random access; in this paper we show how to support fast search as well, thus obtaining an efficient compressed self-index.