Related papers: Succinct Data Structures for Assembling Large Geno…
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…
The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we…
Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…
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…
The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid…
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…
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),…
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
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…
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…
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…
The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the…
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 main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which…
Motivation: Intimately tied to assembly quality is the complexity of the de Bruijn graph built by the assembler. Thus, there have been many paradigms developed to decrease the complexity of the de Bruijn graph. One obvious combinatorial…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
Computing over compressed data combines the space saving of data compression with efficient support for queries directly on the compressed representation. Such data structures are widely applied in text indexing and have been successfully…