Related papers: Read Mapping Near Non-Volatile Memory

Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…

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.…

DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…

DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…

This paper introduces a high-throughput software tool framework called {\it sam2bam} that enables users to significantly speedup pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node…

Computing-in-memory with emerging non-volatile memory (nvCiM) is shown to be a promising candidate for accelerating deep neural networks (DNNs) with high energy efficiency. However, most non-volatile memory (NVM) devices suffer from…

Ternary content addressable memory (TCAM) has been a critical component in caches, routers, etc., in which density, speed, power efficiency, and reliability are the major design targets. There have been the conventional low-write-power but…

Aligning reads to a reference sequence is a fundamental step in numerous bioinformatics pipelines. As a consequence, the sensitivity and precision of the mapping tool, applied with certain parameters to certain data, can critically affect…

Genome modeling conventionally treats gene sequence as a language, reflecting its structured motifs and long-range dependencies analogous to linguistic units and organization principles such as words and syntax. Recent studies utilize…

Convolutional Neural Networks (CNNs), a prominent type of Deep Neural Networks (DNNs), have emerged as a state-of-the-art solution for solving machine learning tasks. To improve the performance and energy efficiency of CNN inference, the…

Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…

Variant detection from high-throughput sequencing data is an essential step in identification of alleles involved in complex diseases and cancer. To deal with these massive data, elaborated sequence analysis pipelines are employed. A core…

Huge numbers of short reads are being generated for mapping back to the genome to discover the frequency of transcripts, miRNAs, DNAase hypersensitive sites, FAIRE regions, nucleosome occupancy, etc. Since these reads are typically short…

Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…

Miniature DNA sequencing hardware has begun to succeed in mobile contexts, driving demand for efficient machine learning at the edge. This domain leverages deep learning techniques familiar from speech and time-series analysis for both…

Motivation: With the development of third-generation sequencing technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce…

Next Generation Sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome…

DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…

At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…

Non-volatile memory (NVM) technologies such as PCM, ReRAM and STT-RAM allow processors to directly write values to persistent storage at speeds that are significantly faster than previous durable media such as hard drives or SSDs. Many…