Compressing genome resequencing data via the Maximal Longest Factor

Abstract

We propose a new algorithm for reference-based compression of genome resequencing data. First, we recap a recent reference-based technique for compressing resequencing data via the Longest Previous Factor (LPF). Viewing the problem from a new light, we call this the Sequential Longest Factor (SLF) method, and introduce improvements to the SLF approach. We further leverage the LPF and propose a new compression method: the Maximal Longest Factor (MLF). For the Homo sapiens genome, our proposed MLF achieves a compression ratio of 486, a significant improvement over 399 (newly improved SLF), 360 (original SLF, Beal, et al., BMC Genomics, 2016), 171 (Pinho, et al., NAR, 2011), and 157 (Wang and Zhang, NAR, 2011).