Related papers: Disk-based genome sequencing data compression
In a distributed information application an encoder compresses an arbitrary vector while a similar reference vector is available to the decoder as side information. For the Hamming-distance similarity measure, and when guaranteed perfect…
Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome…
Large-scale distributed training of Deep Neural Networks (DNNs) on state-of-the-art platforms is expected to be severely communication constrained. To overcome this limitation, numerous gradient compression techniques have been proposed and…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
This study proposes a data condensation method for multivariate kernel density estimation by genetic algorithm. First, our proposed algorithm generates multiple subsamples of a given size with replacement from the original sample. The…
Hand-sized Deoxyribonucleic acid (DNA) sequencing machines are of growing importance in several life sciences fields as their small footprints enable a broader range of use cases than their larger, stationary counterparts. However, as…
Minimizing data storage poses a significant challenge in large-scale metagenomic projects. In this paper, we present a new method for improving the encoding of FASTQ files generated by metagenomic sequencing. This method incorporates…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
We present Quip, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats. In addition to implementing reference-based compression, we have developed, to our knowledge, the first assembly-based…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
Today's sequencing technology allows sequencing an individual genome within a few weeks for a fraction of the costs of the original Human Genome project. Genomics labs are faced with dozens of TB of data per week that have to be…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the errors, a common technique is to include…
This paper presents Bancroft, a computational genomics acceleration platform that provides the illusion of practically infinite on-device memory capacity by compressing genomic data movement over PCIe. Bancroft introduces novel…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…
Digital information can be encoded in the building-block sequence of macro-molecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive.…
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
Deoxyribonucleic acid (DNA) has emerged as a promising building block for next-generation ultra-high density storage devices. Although DNA has high durability and extremely high density in nature, its potential as the basis of storage…
In DNA-based data storage, DNA codes with biochemical constraints and error correction are designed to protect data reliability. Single-stranded DNA sequences with secondary structure avoidance (SSA) help to avoid undesirable secondary…