Related papers: Variable-Order de Bruijn Graphs
Genome rearrangements can be modeled as $k$-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as $2$-breaks, and…
We propose a new algorithm for merging succinct representations of de Bruijn graphs introduced in [Bowe et al. WABI 2012]. Our algorithm is based on the lightweight BWT merging approach by Holt and McMillan [Bionformatics 2014, ACM-BCB…
We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…
Motivation: De Bruijn graphs have been proposed as a data structure to facilitate the analysis of related whole genome sequences, in both a population and comparative genomic settings. However, current approaches do not scale well to many…
An ordered binary decision diagram (OBDD) is a directed acyclic graph that represents a Boolean function. OBDDs are also known as special cases of oblivious read-once branching programs in the field of complexity theory. Since OBDDs have…
A universal cycle for a set S of combinatorial objects is a cyclic sequence of length |S|that contains a representation of each element in S exactly once as a substring. If S is the set of k-subsets of [n] = {1, 2, . . . , n}, it is…
Searching for other participants is one of the most important operations in a distributed system. We are interested in topologies in which it is possible to route a packet in a fixed number of hops until it arrives at its destination. Given…
Orientable sequences of order n are infinite periodic sequences with symbols drawn from a finite alphabet of size k with the property that any particular subsequence of length n occurs at most once in a period in either direction. They were…
Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…
Degree-based graph construction is an ubiquitous problem in network modeling, ranging from social sciences to chemical compounds and biochemical reaction networks in the cell. This problem includes existence, enumeration, exhaustive…
Motivations Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large data sets or…
Many applications donot have the benefit of the laws of physics to derive succinct descriptive models for observed data. In alternative, interdependencies among $N$ time series $\{ x_{nk}, k>0 \}_{n=1}^{N}$ are nowadays often captured by a…
A universal cycle for a set S of combinatorial objects is a cyclic sequence of length |S| that contains a representative of each element in S exactly once as a substring. Despite the many universal cycle constructions known in the…
Graphs play an increasingly important role in various big data applications. However, existing graph data structures cannot simultaneously address the performance bottlenecks caused by the dynamic updates, large scale, and high query…
Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input strings. The motivations for those results stem from…
In this article, we show how to transform a colored de Bruijn graph (dBG) into a practical index for processing massive sets of sequencing reads. Similar to previous works, we encode an instance of a colored dBG of the set using BOSS and a…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…
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…
A graph $G$ is called self-ordered (a.k.a asymmetric) if the identity permutation is its only automorphism. Equivalently, there is a unique isomorphism from $G$ to any graph that is isomorphic to $G$. We say that $G=(V,E)$ is robustly…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…