# PLORC: A Pipelined Lossless Reference-Free Compression Architecture for FASTQ Files
## 1 Introduction
[PERSON] proposed a reference-based genomic alignment (REBA) method to perform genomic compression on FPGA in [16]. This method can achieve a better compression ratio than reference-free compression algorithms. 'Reference-based' algorithms require a genome  
Figure 1: An example of a genomic analysis system. sequence reference used as a dictionary to compress, while'reference-free' algorithms do not need a genomic reference. However, storing the reference sequence and frequent memory access consume a great deal of power and hardware resources. In addition, looking up in the reference introduces unpredictable latency, which limits its throughput rate. The high resource and power consumption decrease the flexibility and reusability of the algorithm, which makes further parallel implementation difficult. Moreover, the decompression method was not proposed in [16]. In summary, when facing the challenge of online compression for genomic data, current genomic compression algorithms present several limitations:  
* The CPU-based general and genomic-specific compression algorithms typically occupy multiple CPU cores while delivering limited processing speed. Therefore, these algorithms cannot achieve online compression and decompression. * The FPGA-based general and reference-based compression algorithms tend to consume significant memory resources and require frequent memory access. Furthermore, our evaluations reveal that FPGA-based general-purpose compression algorithms yield suboptimal compression ratios when applied to FASTQ files. * Existing studies primarily emphasize the acceleration of compression algorithms, with little attention given to the optimization or acceleration of decompression algorithms. To address these issues, we propose PLORC, a novel Pipelined Lossless Reference-free Compression architecture, comprising both a compressor and a decompressor, specially designed for streaming genomic data in a FASTQ format. The main contributions of our work are as follows:  
* We designed a fully pipelined architecture of the compressor and decompressor for streaming genomic data in a FASTQ format. All the modules were specially designed and built according to the structure of FASTQ files and the features of FPGA. As far as we know, PLORC is the first FPGA-based pipelined reference-free FASTQ compression architecture. * The PLORC compressor achieved the best throughput rate among the representative algorithms we tested, while the decompressor matched the high throughput rate, maintaining balanced performance. * PLORC demonstrated superior resource utilization and power efficiency compared to the FPGA-based algorithms evaluated in this study. * The PLORC compressor surpassed some common general-purpose algorithms in terms of the compression ratio. This paper is organized as follows: Section 2 provides a detailed explanation of the PLORC compressor and its hardware implementation. Section 3 discusses the PLORC compressor and its corresponding hardware architecture. Section 4 presents the experimental results and discusses the findings. Finally, Section 5 concludes the paper and outlines directions for future work.