Related papers: Memory Efficient De Bruijn Graph Construction
De novo assembly enables investigations of unknown genomes, paving the way for personalized medicine and disease management. However, it faces immense computational challenges arising from the excessive data volumes and algorithmic…
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.…
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 $O(n \log g)$…
Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long…
We present Quip, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats. In addition to implementing reference-based compression, we have developed, to our knowledge, the first assembly-based…
Motivation: Building the histogram of occurrences of every $k$-symbol long substring of nucleotide data is a standard step in many bioinformatics applications, known under the name of $k$-mer counting. Its applications include developing de…
De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of…
In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the…
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…
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…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
In this paper, we address the problem of recovering arbitrary-shaped data clusters from datasets while facing \emph{high space constraints}, as this is for instance the case in many real-world applications when analysis algorithms are…
In many models for large-scale computation, decomposition of the problem is key to efficient algorithms. For distance-related graph problems, it is often crucial that such a decomposition results in clusters of small diameter, while the…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…
Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…
The reduction of the fragment assembly problem to (variations of) the classical Eulerian trail problem [Pevzner et al., PNAS 2001] has led to remarkable progress in genome assembly. This reduction employs the notion of de Bruijn graph…
This paper is focused in designing an efficient on-line algorithm to reconstruct a DNA sequence and search the genes in it, we assume that the segment have no mutation or reading error, the algorithm is based on de Bruijn Graph for…