Related papers: Space efficient merging of de Bruijn graphs and Wh…
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 present a succinct data structure for permutation graphs, and their superclass of circular permutation graphs, i.e., data structures using optimal space up to lower order terms. Unlike concurrent work on circle graphs (Acan et al. 2022),…
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…
In recent years several compressed indexes based on variants of the Burrows-Wheeler transformation have been introduced. Some of these index structures far more complex than a single string, as was originally done with the FM-index…
We propose new graph representations that exploit dense local structure to improve time and space simultaneously. Given an undirected graph $G$, we define a dual clique cover (DCC) representation of $G$ to be the pair $(C, L)$, where $C$ is…
This paper introduces the de Bruijn graph edge minimization problem, which is related to the compression of de Bruijn graphs: find the order-k de Bruijn graph with minimum edge count among all orders. We describe an efficient algorithm that…
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…
In this paper we propose a flexible and lightweight technique for merging compressed indices based on variants of Burrows-Wheeler transform (BWT), thus addressing the need for algorithms that compute compressed indices over large…
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…
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 $G_K$ 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…
Structural decomposition methods offer powerful theoretical guarantees for join evaluation, yet they are rarely used in real-world query optimizers. A major reason is the difficulty of combining cost-based plan search and structure-based…
Kautz and de Bruijn graphs have a high degree of connectivity which makes them ideal candidates for massively parallel computer network topologies. In order to realize a practical computer architecture based on these graphs, it is useful to…
Real-world optimization problems are generally not just black-box problems, but also involve mixed types of inputs in which discrete and continuous variables coexist. Such mixed-space optimization possesses the primary challenge of modeling…
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…
Graph similarity search has received considerable attention in many applications, such as bioinformatics, data mining, pattern recognition, and social networks. Existing methods for this problem have limited scalability because of the huge…
We present a novel space-efficient graph coarsening technique for $n$-vertex planar graphs $G$, called cloud partition, which partitions the vertices $V(G)$ into disjoint sets $C$ of size $O(\log n)$ such that each $C$ induces a connected…
For the first time we provide a succinct pattern matching index for arbitrary graphs that can be built in polynomial time, which requires less space and answers queries more efficiently than the one in [SODA 2021]. We show that, given an…
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…
We describe an algorithm for compressing a partially ordered set, or \emph{poset}, so that it occupies space matching the information theory lower bound (to within lower order terms), in the worst case. Using this algorithm, we design a…