相关论文: Barnacle: An Assembly Algorithm for Clone-based Se…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
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 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…
Background: The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required…
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…
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…
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly,…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
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…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…
A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
Most genome assemblers construct point estimates, choosing a genome sequence from among many alternative hypotheses that are supported by the data. We present a Markov Chain Monte Carlo approach to sequence assembly that instead generates…
Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of…
Aiming to generate easy-to-handle assembly sequences for robotic assembly, this study tackles assembly sequence generation by considering two tradeoff objectives: (1) insertion conditions and (2) degrees of constraints among assembled…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…
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…
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…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…