Quality Scores Compression of Genomic Sequencing Data: A Comprehensive Review and Performance Evaluation

Advanced sequencing technologies have profoundly revolutionized biology and produced vast amounts of raw sequencing data during the past decades. The enormous amount of sequencing data proposed significant challenges of data storage and transmission. Compressing a big file into a small file is an encouraging method to tackle these challenges. Howver, it has been found that traditional text data compression algorithms are not well-suited for handing the vast sequencing datasets. Therefore, several algorithms are designed specifically for the efficient compression of sequencing data. Recently, considerable research has been devoted to compressing quality scores stored in the FASTQ format file, resulting in substantial advances in compression performance. Despite these advances, there has been no systematic review and evaluation of these algorithms or software. In this review, we aim to conduct a broad review of the existing quality score compression algorithms. We mainly discuss those algorithms from two categories, i.e., lossless and lossy compression. Additionally, we benchmark the compression performance of 12 tools using 14 real datasets. We anticipate that our review will provide practical guidance for others seeking to design an appropriate algorithm for compressing quality scores.