Related papers: An Index for Sequencing Reads Based on The Colored…
We present an index structure, called the color-index, to boost the evaluation of acyclic conjunctive queries (ACQs) over binary schemas. The color-index is based on the color refinement algorithm, a widely used subroutine for graph…
De Bruijn graphs are essential for sequencing data analysis and must be efficiently constructed and stored for large-scale population studies. They also need to be dynamic to allow updates such as adding or removing edges and nodes.…
De novo DNA assembly is a fundamental task in Bioinformatics, and finding Eulerian paths on de Bruijn graphs is one of the dominant approaches to it. In most of the cases, there may be no one order for the de Bruijn graph that works well…
Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…
Motivation: Working with a large number of genomes simultaneously is of great interest in genetic population and comparative genomics research. Bubbles discovery in multi-genomes coloured de bruijn graph for de novo genome assembly is a…
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…
Identifying the sets of operations that can be executed simultaneously is an important problem appearing in many parallel applications. By modeling the operations and their interactions as a graph, one can identify the independent…
De Bruijn graph is one of the most important data structures used in de-novo genome assembly algorithms, especially for NGS data. There is a growing need for parallel data structures and algorithms due to the increasing number of cores in…
De Brujin graphs are widely used in bioinformatics for processing next-generation sequencing data. Due to a very large size of NGS datasets, it is essential to represent de Bruijn graphs compactly, and several approaches to this problem…
The de Bruijn graph plays an important role in bioinformatics, especially in the context of de novo assembly. However, the representation of the de Bruijn graph in memory is a computational bottleneck for many assemblers. Recent papers…
The de Bruijn graph, its sequences, and their various generalizations, have found many applications in information theory, including many new ones in the last decade. In this paper, motivated by a coding problem for emerging memory…
Variation graphs, which represent genetic variation within a population, are replacing sequences as reference genomes. Path indexes are one of the most important tools for working with variation graphs. They generalize text indexes to…
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 merging of succinct data structures is a well established technique for the space efficient construction of large succinct indexes. In the first part of the paper we propose a new algorithm for merging succinct representations of de…
Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotgun sequencing data from these complex populations are an…
In this paper, we present multi-threaded algorithms for graph coloring suitable to the shared memory programming model. We modify an existing algorithm widely used in the literature and prove the correctness of the modified algorithm. We…
The problem of counting occurrences of query graphs in a large data graph, known as subgraph counting, is fundamental to several domains such as genomics and social network analysis. Many important special cases (e.g. triangle counting)…
The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs.…
We study the problem of coloring a given graph using a small number of colors in several well-established models of computation for big data. These include the data streaming model, the general graph query model, the massively parallel…
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…