Comparative studies on the high-performance compression of SARS-CoV-2 genome collections

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is fast mutating worldwide. The mutated strains have been timely sequenced by worldwide labs, accumulating a huge amount of viral genome sequences open to public for biomedicine research such as mRNA vaccine design and drug recommendation. It is inefficient to transmit the millions of genome sequences without compression. In this study, we benchmark the performance of reference-free and reference-based compression algorithms on SARS-CoV-2 genome collections extracted from NCBI. Experimental results show that reference-based two-level compression is the most suitable approach to the compression, achieving the best compression ratio 1019.33-fold for compressing 132 372 genomes and 949.73-fold for compressing 416 238 genomes. This enormous file size reduction and efficient decompression have enabled a 5-min download and decompression of $10^5$ SARS-CoV-2 genomes. As compression on datasets containing such big numbers of genomes has been explored seldom before, our comparative analysis of the state-of-the-art compression algorithms provides practical guidance for the selection of compression tools and their parameters such as reference genomes to compress viral genome databases with similar characteristics. We also suggested a genome clustering approach using multiple references for a better compression. It is anticipated that the increased availability of SARS-CoV-2 genome datasets will make biomedicine research more productive.