Related papers: Disk-based genome sequencing data compression

DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…

Genome sequence analysis, which examines the DNA sequences of organisms, drives advances in many critical medical and biotechnological fields. Given its importance and the exponentially growing volumes of genomic sequence data, there are…

As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in…

High-throughput DNA sequencers are becoming indispensable in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous…

DNA exhibits remarkable potential as a data storage solution due to its impressive storage density and long-term stability, stemming from its inherent biomolecular structure. However, developing this novel medium comes with its own set of…

Motivation: High-throughput sequencing (HTS) enables population-scale genomics but generates massive datasets, creating bottlenecks in storage, transfer, and analysis. FASTQ, the standard format for over two decades, stores one byte per…

DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…

De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…

Since the release of human genome sequences, one of the most important research issues is about indexing the genome sequences, and the suffix tree is most widely adopted for that purpose. The traditional suffix tree construction algorithms…

Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…

As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…

Compression is a crucial solution for data reduction in modern scientific applications due to the exponential growth of data from simulations, experiments, and observations. Compression with progressive retrieval capability allows users to…

As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential…

Sequential data is being generated at an unprecedented pace in various forms, including text and genomic data. This creates the need for efficient compression mechanisms to enable better storage, transmission and processing of such data. To…

In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…

The exponential increase in storage demand and low lifespan of data storage devices has resulted in long-term archival and preservation emerging as a critical bottlenecks in data storage. In order to meet this demand, researchers are now…

The multidimensional databases often use compression techniques in order to decrease the size of the database. This paper introduces a new method called difference sequence compression. Under some conditions, this new technique is able to…

Motivation: FASTQ is a standard file format for DNA sequencing data which stores both nucleotides and quality scores. A typical sequencing study can easily generate hundreds of gigabytes of FASTQ files, while public archives such as ENA and…

Diffraction drastically limits the bit density in optical data storage. To increase the storage density, alternative strategies involving supplementary recording dimensions and robust read-out schemes must be explored. Here, we propose to…