Related papers: Lock-free de Bruijn graph
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…
Massively parallel DNA sequencing technologies are revolutionizing genomics research. Billions of short reads generated at low costs can be assembled for reconstructing the whole genomes. Unfortunately, the large memory footprint of the…
Motivation: Data volumes generated by next-generation sequencing technolo- gies is now a major concern, both for storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as…
Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures 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…
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…
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 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…
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…
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…
Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an $O(n \log g)$…
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: 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…
Graph algorithms applied in many applications, including social networks, communication networks, VLSI design, graphics, and several others, require dynamic modifications -- addition and removal of vertices and/or edges -- in the graph.…
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…
Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome…
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.…
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.…
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…
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…