Related papers: SW# - GPU enabled exact alignments on genome scale

Genetic Programming (GP), an evolutionary learning technique, has multiple applications in machine learning such as curve fitting, data modelling, feature selection, classification etc. GP has several inherent parallel steps, making it an…

Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…

BarraCUDA is a C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. The genetically improved (GI) code is up to three times faster on short paired end…

In recent years, the rapidly increasing number of reads produced by next-generation sequencing (NGS) technologies has driven the demand for efficient implementations of sequence alignments in bioinformatics. However, current…

We present an assignment for a full Parallel Computing course. Since 2017/2018, we have proposed a different problem each academic year to illustrate various methodologies for approaching the same computational problem using different…

Genetic Algorithms (GAs) are used to solve search and optimization problems in which an optimal solution can be found using an iterative process with probabilistic and non-deterministic transitions. However, depending on the problem's…

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for…

These notes accompany the open-source code published in GitHub which implements a GPU-based line-segment, surface-triangle intersection algorithm in CUDA. It mentions some relevant works and discusses issues specific to this implementation.…

Calculating the similarities between a pair of genomic sequences is one of the most fundamental computational steps in genomic analysis. This step -- called sequence alignment -- is the computational bottleneck because: (1) it is…

The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a…

We present a new adaptive parallel algorithm for the challenging problem of multi-dimensional numerical integration on massively parallel architectures. Adaptive algorithms have demonstrated the best performance, but efficient many-core…

I present a new GPU implementation of the wavelet tree data structure. It includes binary rank and select support structures that provide at least 10 times higher throughput of binary rank and select queries than the best publicly available…

At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the…

This paper presents the implementation of a quantum sequence alignment (QSA) algorithm on biological data in environments simulating noisy intermediate-scale quantum (NISQ) computers. The approach to quantum bioinformatics adapts the…

This paper presents GPU performance optimization and scaling results for inference models of the Sparse Deep Neural Network Challenge 2020. Demands for network quality have increased rapidly, pushing the size and thus the memory…

GPUs have significantly accelerated first-order methods for large-scale optimization, especially in continuous optimization. However, this success has not transferred cleanly to problems with discrete variables, combinatorial structure, and…

We describe the GPU implementation of shifted or multimass iterative solvers for sparse linear systems of the sort encountered in lattice gauge theory. We provide a generic tool that can be used by those without GPU programming experience…

We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent…

Graphics Processing Unit, or GPUs, have been successfully adopted both for graphic computation in 3D applications, and for general purpose application (GP-GPUs), thank to their tremendous performance-per-watt. Recently, there is a big…

Sequence alignment is a memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory architectures alleviate this bottleneck by providing the memory with computing…