12 papers · ranked by Valyu relevance
Ge Zhang
bcftools is the standard toolkit for handling VCF and BCF variant files, but it processes records on a single core; its --threads option speeds up only compression of the output, not the work done on variant records. Processing large call sets is therefore slow, and users often divide the genome and reassemble the…
Rafael Terra, Diego Carvalho, Denis Jacob Machado, Carla Osthoff + 1 more
Advances in High-Performance Computing (HPC) have enabled increasingly complex genomic analyses, including those in phylogenomics. These analyses contribute to understanding the evolution of viruses and pathogens, improving our knowledge of disease transmission, and supporting targeted public health strategies.…
Kecong Tang, Ardalan Naseri, Degui Zhi, Shaojie Zhang + 1 more
To support memory-efficient execution without compromising the all-vs.-all nature of IBD detection, RaPID2 adopts a partitioning strategy that operates on haplotype pairs () rather than subpanels. All pairs are normalized such that $A<B$ to ensure consistent key assignment, and each pair is deterministically assigned…
Bahman Arasteh, Seyed Salar Sefati, Huseyin Kusetogullari, Farzad Kiani + 3 more
Efficient task scheduling remains a key challenge in High-Performance Computing and Internet of Things (IoT) systems, where the sequential execution of nested loops often limits parallelism. This paper proposes a hybrid approach that dynamically parallelizes nested loops in heterogeneous IoT environments. The suggested…
Zhejian Yu
Fast simulation of next-generation sequencing (NGS) data is vital for software development and benchmarking. Here we describe art_modern, an accelerated ART simulator that can simulate various NGS data. We accelerated ART using updated sampling algorithms, single-instruction multiple-data (SIMD) instruction-set…
Mohammed Alaa Ala’anzy, Nurdaulet Tolendi, Baizhan Baubek, Abdulmohsen Algarni + 1 more
Sorting can be approached in two main ways: sequentially and in parallel. In sequential sorting, data is processed in a single-threaded manner, which can be slow for large datasets. However, parallel sorting divides the task across multiple processing units, enabling faster results by processing data simultaneously.…
Rob Patro, Siddhant Bharti, Prajwal Singhania, Rakrish Dhakal + 2 more
The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compressed fastq.gz files has become a substantial scalability bottleneck in the modern world of fast and massively parallel…
John Kruper, Ariel Rokem
Tractography based on diffusion-weighted MRI (dMRI) is the predominant in vivo method for mapping the brain’s white matter. However, it is also one of the most computationally demanding steps in neuroimaging data analysis-requiring the generation and filtering of millions of streamlines per subject. Over the past…
Noam Teyssier, Alexander Dobin
Single-cell genomics is rapidly scaling toward billion-cell atlases, but computational analysis has become a critical bottleneck. Processing multiplexed datasets with existing tools requires substantial computational resources and runtime that become prohibitive at scale. Here we present cyto, an ultra highthroughput…
Mateusz Gruzewski, Marek Palkowski, Ramon Antonio Rodriges Zalipynis
In this article, we present an efficient and concise OpenMP implementation of the Nussinov RNA folding algorithm, a well-known representative of non-serial polyadic dynamic programming (NPDP). Our goal is to develop an optimized implementation that can serve as a template for related dynamic programming applications.…
Ismail Melik Turker, Isa Yildirim
3.3.1#### Experimental setup All experiments were conducted on a laptop running Ubuntu 24.04 LTS, equipped with an Intel Core i7-12700H processor (12th generation, Alder Lake hybrid architecture with 6 performance and 8 efficient cores) and 64 GB of DDR4 memory. The code was written entirely in C++17 and parallelized…
Anders Pitman, Cathy Yang, Yi Qiao
Next-generation sequencing now produces whole-genome data in hours, but downstream variant calling remains a multi-hour to multi-day bottleneck that excludes genomic analysis from time-critical clinical settings. GPU acceleration offers a natural path forward — variant calling is inherently parallelizable across…