Related papers: Read Mapping on de Bruijn graph

Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…

DNA technologies have evolved significantly in the past years enabling the sequencing of a large number of genomes in a short time. Nevertheless, the underlying computational problem is hard, and many technical factors and limitations…

The de Bruijn graph $G_K$ of a set of strings $S$ is a key data structure in genome assembly that represents overlaps between all the $K$-length substrings of $S$. Construction and navigation of the graph is a space and time bottleneck in…

de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which…

Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…

The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…

The formal version of our work has been published in BMC Bioinformatics and can be found here: http://www.biomedcentral.com/1471-2105/13/S6/S1 Motivation: To tackle the problem of huge memory usage associated with de Bruijn graph-based…

Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long…

Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…

Graph Neural Networks (GNNs) are exemplary deep models designed for graph data. Message passing mechanism enables GNNs to effectively capture graph topology and push the performance boundaries across various graph tasks. However, the trend…

The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…

A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…

Genome analysis has revolutionized fields such as personalized medicine and forensics. Modern sequencing machines generate vast amounts of fragmented strings of genome data called reads. The alignment of these reads into a complete DNA…

Current applications have produced graphs on the order of hundreds of thousands of nodes and millions of edges. To take advantage of such graphs, one must be able to find patterns, outliers and communities. These tasks are better performed…

Graph neural networks (GNNs) demonstrate a robust capability for representation learning on graphs with complex structures, showcasing superior performance in various applications. The majority of existing GNNs employ a graph convolution…

We introduce De Bruijn Graph Neural Networks (DBGNNs), a novel time-aware graph neural network architecture for time-resolved data on dynamic graphs. Our approach accounts for temporal-topological patterns that unfold in the causal topology…

Multi-hop reading comprehension focuses on one type of factoid question, where a system needs to properly integrate multiple pieces of evidence to correctly answer a question. Previous work approximates global evidence with local…

Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…

The advent of Graph Neural Networks (GNNs) has revolutionized the field of machine learning, offering a novel paradigm for learning on graph-structured data. Unlike traditional neural networks, GNNs are capable of capturing complex…

Graph neural networks (GNNs) emerged recently as a standard toolkit for learning from data on graphs. Current GNN designing works depend on immense human expertise to explore different message-passing mechanisms, and require manual…