Related papers: MaxSSmap: A GPU program for mapping divergent shor…

There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…

Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…

Sequence alignment is one of the oldest and the most famous problems in bioinformatics. Even after 45 years, for one reason or another, this problem is still actual; current solutions are trade-offs between execution time, memory…

We propose an incomplete algorithm for Maximum Satisfiability (MaxSAT) specifically designed to run on neural network accelerators such as GPUs and TPUs. Given a MaxSAT problem instance in conjunctive normal form, our procedure constructs a…

A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…

We improve on GenASM, a recent algorithm for genomic sequence alignment, by significantly reducing its memory footprint and bandwidth requirement. Our algorithmic improvements reduce the memory footprint by 24$\times$ and the number of…

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…

Subgraph matching is a core operation in graph analytics, supporting a broad spectrum of applications from social network analysis to bioinformatics. Recent GPU-based approaches accelerate subgraph matching by leveraging parallelism but…

Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many…

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…

We present Masai, a read mapper representing the state of the art in terms of speed and sensitivity. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2--3 times faster and more accurate than Bowtie 2 and BWA. The novelties…

In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…

In this paper we introduce a novel parallel pipeline for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, named HPG-Aligner, leverages the speed of the Burrows-Wheeler Transform to map…

Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…

This paper presents an accurate short-read mapper for next-generation sequencing data which is widely used in the 1000 Genomes Project, and human clinical and other species genome studies.

Background Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig…

Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -- called short reads -- that cause significant computational burden. To analyze the entire genome, each of the billions of…

Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…

Set intersection is the core in a variety of problems, e.g. frequent itemset mining and sparse boolean matrix multiplication. It is well-known that large speed gains can, for some computational problems, be obtained by using a graphics…

Summary: The Smith Waterman (SW) algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools, but current implementations…