Learning-based compression shows competitive compression ratios for genomics data. It often includes three types of compressors: static, adaptive and semi-adaptive. However, these existing compressors suffer from inferior compression ratios or throughput, and adaptive compressors also faces model cold-start problems. To address these issues, we propose DeepGeCo, a novel genomics data lossless adaptive compression framework with (s,k)-mer encoding and deep neural networks, involving three compression modes (MINI for static, PLUS for adaptive, ULTRA for semi-adaptive) for flexible requirements of compression ratios or throughput. In DeepGeCo, (1) we develop BiGRU and Transformer as the backbone to build Warm-Start and Supporter models in terms of cold-start problems. (2) We introduce (s,k)-mer encoding to pre-process genomics data before feeding it into the DNN model for improve model throughput, and we propose a new metric - Ranking of Throughput and Compression Ratio (RTCR) for effective encoding parameters selection. (3) We design a threshold controller and a probabilistic mixer within the backbone to balance compression ratios and model throughput. Experiments on 10 real-world datasets show that DeepGeCo's three compression modes improve up to a 22.949X average throughput and up to a 31.095% average compression ratio improvement while occupying low CPU or GPU memory.

The advancement of long reads sequencing technologies has led to a significant increase in biological sequencing big data. Although several reference-free compressors are available for saving long reads data storage space, choosing the suitable one is challenging due to the shortage of thorough and systematic evaluations of their lossless compression effectiveness, both dedicated and general-purpose. In this study, we performed benchmark examinations on 30 compressors, including 11 specialized for long reads and 19 general-purpose ones, using 31 real-world datasets with differing sequencing platforms, species, and lengths. Each lossless compressor was evaluated on 13 performance measures, including compression strength, compression robustness, as well as time and peak memory required for compression and decompression. Additionally, for future long reads data compressors, we outlined investigation directions with consideration for privacy-sensitive sequences data security, hardware parallel acceleration, parameter tuning framework, and system hardware-algorithm integration design. We summarized the results as the Long Reads Compression Benchmark, available at https://github.com/fahaihi/LRCB.

MOTIVATION: The quality scores data (QSD) account for 70% in compressed FastQ files obtained from the short and long reads sequencing technologies. Designing effective compressors for QSD that counterbalance compression ratio, time cost, and memory consumption is essential in scenarios such as large-scale genomics data sharing and long-term data backup. This study presents a novel parallel lossless QSD-dedicated compression algorithm named PQSDC, which fulfills the above requirements well. PQSDC is based on two core components: a parallel sequences-partition model designed to reduce peak memory consumption and time cost during compression and decompression processes, as well as a parallel four-level run-length prediction mapping model to enhance compression ratio. Besides, the PQSDC algorithm is also designed to be highly concurrent using multicore CPU clusters. RESULTS: We evaluate PQSDC and four state-of-the-art compression algorithms on 27 real-world datasets, including 61.857 billion QSD characters and 632.908 million QSD sequences. (1) For short reads, compared to baselines, the maximum improvement of PQSDC reaches 7.06% in average compression ratio, and 8.01% in weighted average compression ratio. During compression and decompression, the maximum total time savings of PQSDC are 79.96% and 84.56%, respectively; the maximum average memory savings are 68.34% and 77.63%, respectively. (2) For long reads, the maximum improvement of PQSDC reaches 12.51% and 13.42% in average and weighted average compression ratio, respectively. The maximum total time savings during compression and decompression are 53.51% and 72.53%, respectively; the maximum average memory savings are 19.44% and 17.42%, respectively. (3) Furthermore, PQSDC ranks second in compression robustness among the tested algorithms, indicating that it is less affected by the probability distribution of the QSD collections. Overall, our work provides a promising solution for QSD parallel compression, which balances storage cost, time consumption, and memory occupation primely. AVAILABILITY AND IMPLEMENTATION: The proposed PQSDC compressor can be downloaded from https://github.com/fahaihi/PQSDC.

The current redundant sequence deduplication algorithms cannot remove structural repetitive DNA short reads such as mirror, reverse, paired, and complementary palindromes in high-throughput genomics sequencing data. Moreover, these methods also cannot construct indexes to recover the original sequences, thus failing to meet the requirements of lossless compression for downstream applications. To address these problems, we propose a data structure called Cycle-Hash-Linkage (CHL) and present a CPU parallelism optimization algorithm named SR2C (Structurally Redundant Short Reads Collapser) based on CHL to improve the compression ratio of DNA sequencing data. Experimental results on actual data from the NCBI database demonstrate that SR2C achieves an average residual sequence percentage improvement of 2.556% compared to the state-of-the-art redundant sequence deduplication algorithm, Minirmd. Furthermore, SR2C cascaded optimization improves the average compression ratios of compression algorithms Pigz, PBzip2, XZ, and 7Z by 92.345%, 78.999%, 10.132%, and 7.434%, respectively. By leveraging multi-core CPU parallel computation, SR2C effectively reduces time consumption, which achieves 2-5X deduplication and recovers acceleration.The same name Linux toolkit is freely available at https://github.com/fahaihi/SR2C.

BACKGROUND: Genomic sequencing reads compressors are essential for balancing high-throughput sequencing short reads generation speed, large-scale genomic data sharing, and infrastructure storage expenditure. However, most existing short reads compressors rarely utilize big-memory systems and duplicative information between diverse sequencing files to achieve a higher compression ratio for conserving reads data storage space. RESULTS: We employ compression ratio as the optimization objective and propose a large-scale genomic sequencing short reads data compression optimizer, named PMFFRC, through novelty memory modeling and redundant reads clustering technologies. By cascading PMFFRC, in 982 GB fastq format sequencing data, with 274 GB and 3.3 billion short reads, the state-of-the-art and reference-free compressors HARC, SPRING, Mstcom, and FastqCLS achieve 77.89%, 77.56%, 73.51%, and 29.36% average maximum compression ratio gains, respectively. PMFFRC saves 39.41%, 41.62%, 40.99%, and 20.19% of storage space sizes compared with the four unoptimized compressors. CONCLUSIONS: PMFFRC rational usage big-memory of compression server, effectively saving the sequencing reads data storage space sizes, which relieves the basic storage facilities costs and community sharing transmitting overhead. Our work furnishes a novel solution for improving sequencing reads compression and saving storage space. The proposed PMFFRC algorithm is packaged in a same-name Linux toolkit, available un-limited at https://github.com/fahaihi/PMFFRC .