Related papers: GeneZip: A software package for storage-efficient …
We present a Compression Tool, "GenBit Compress", for genetic sequences based on our new proposed "GenBit Compress Algorithm". Our Tool achieves the best compression ratios for Entire Genome (DNA sequences) . Significantly better…
With the reduction of sequencing costs and the pervasiveness of computing devices, genomic data collection is continually growing. However, data collection is highly fragmented and the data is still siloed across different repositories.…
In a world with data that change rapidly and abruptly, it is important to detect those changes accurately. In this paper we describe an R package implementing a generalized version of an algorithm recently proposed by Hocking et al. [2020]…
Current network data telemetry pipelines consist of massive streams of fine-grained Key Performance Indicators (KPIs) from multiple distributed sources towards central aggregators, making data storage, transmission, and real-time analysis…
Pedigree data contain family history information that is used to analyze hereditary diseases. These clinical data sets may contain duplicate records due to the same family visiting a clinic multiple times or a clinician entering multiple…
Advances in DNA sequencing technology will soon result in databases of thousands of genomes. Within a species, individuals' genomes are almost exact copies of each other; e.g., any two human genomes are 99.9% the same. Relative Lempel-Ziv…
We describe a new algorithm and R package for peak detection in genomic data sets using constrained changepoint algorithms. These detect changes from background to peak regions by imposing the constraint that the mean should alternately…
Genotype imputation enhances genetic data by predicting missing SNPs using reference haplotype information. Traditional methods leverage linkage disequilibrium (LD) to infer untyped SNP genotypes, relying on the similarity of LD structures…
Compression techniques that support fast random access are a core component of any information system. Current state-of-the-art methods group documents into fixed-sized blocks and compress each block with a general-purpose adaptive…
Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in…
Explosive growth in the amount of genomic data is matched by increasing power of consumer-grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative…
Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes…
Non-sharable sensitive data collection and analysis in large-scale consortia for genomic research is complicated. Time consuming issues in installing software arise due to different operating systems, software dependencies and running the…
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,…
Genome Wide Association Studies (GWAS) are used to identify statistically significant genetic variants in case-control studies. GWAS typically use a p-value threshold of 5 x 10-8 to identify highly ranked single nucleotide polymorphisms…
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…
Motivation: Data volumes generated by next-generation sequencing technolo- gies is now a major concern, both for storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as…
Haplotype phasing, the process of resolving parental allele inheritance patterns in diploid genomes, is critical for precision medicine and population genetics, yet the underlying optimization is NP-hard, posing a scalability challenge. To…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
Gzip is a file compression format, which is ubiquitously used. Although a multitude of gzip implementations exist, only pugz can fully utilize current multi-core processor architectures for decompression. Yet, pugz cannot decompress…