Related papers: Fast Processing and Querying of 170TB of Genomics …
The recent super-exponential growth in the amount of sequencing data generated worldwide has put techniques for compressed storage into the focus. Most available solutions, however, are strictly tied to specific bioinformatics formats,…
With the explosion of information stored world-wide,data intensive computing has become a central area of research.Efficient management and processing of this massively exponential amount of data from diverse sources,such as…
Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotgun sequencing data from these complex populations are an…
Large-scale genomic workflows used in precision medicine can process datasets spanning tens to hundreds of gigabytes per sample, leading to high memory spikes, intensive disk I/O, and task failures due to out-of-memory errors. Simple static…
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…
A retrieval data structure stores a static function f : S -> {0,1}^r . For all x in S, it returns the r-bit value f(x), while for other inputs it may return an arbitrary result. The structure cannot answer membership queries, so it does not…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
This paper presents a novel method for efficient image retrieval, based on a simple and effective hashing of CNN features and the use of an indexing structure based on Bloom filters. These filters are used as gatekeepers for the database of…
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…
Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…
Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…
Next Generation Sequencing (NGS) platforms and, more generally, high-throughput technologies are giving rise to an exponential growth in the size of nucleotide sequence databases. Moreover, many emerging applications of nucleotide datasets…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid…
We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…
Bloom Filter is an important probabilistic data structure to reduce memory consumption for membership filters. It is applied in diverse domains such as Computer Networking, Network Security and Privacy, IoT, Edge Computing, Cloud Computing,…
Advances in genome sequencing technologies generate massive amounts of sequence data that are increasingly analyzed and shared through public repositories. On-demand infrastructure services on cloud computing platforms enable the processing…
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…
A Bloom Filter is a probabilistic data structure designed to check, rapidly and memory-efficiently, whether an element is present in a set. It has been vastly used in various computing areas and several variants, allowing deletions, dynamic…
Organizations handling sensitive documents face a tension: cloud-based AI risks GDPR violations, while local systems typically require 18-32 GB RAM. This paper presents CUBO, a systems-oriented RAG platform for consumer laptops with 16 GB…