Relative Lempel-Ziv Compression of Genomes for Large-Scale Storage and Retrieval

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Abstract

Self-indexes – data structures that simultaneously provide fast search of and access to compressed text – are promising for genomic data but in their usual form are not able to exploit the high level of replication present in a collection of related genomes. Our ‘RLZ’ approach is to store a self-index for a base sequence and then compress every other sequence as an LZ77 encoding relative to the base. For a collection of r sequences totaling N bases, with a total of s point mutations from a base sequence of length n, this representation requires just \(nH_k(T) + s\log n + s\log \frac{N}{s} + O(s)\) bits. At the cost of negligible extra space, access to ℓ consecutive symbols requires \(\O(\ell + \log n)\) time. Our experiments show that, for example, RLZ can represent individual human genomes in around 0.1 bits per base while supporting rapid access and using relatively little memory.

This work was supported by the Australian Research Council and the NICTA Victorian Research Laboratory. NICTA is funded by the Australian Government as represented by the Department of Broadband, Communications and the Digital Economy and the Australian Research Council through the ICT Center of Excellence program.