Related papers: QuorUM: an error corrector for Illumina reads
We introduce an improved version of RECKONER, an error corrector for Illumina whole genome sequencing data. By modifying its workflow we reduce the computation time even 10 times. We also propose a new method of determination of $k$-mer…
Motivation: Next-generation sequencing tools have enabled producing of huge amount of genomic information at low cost. Unfortunately, presence of sequencing errors in such data affects quality of downstream analyzes. Accuracy of them can be…
Summary: We present a new tool to correct sequencing errors in Illumina data produced from high-coverage whole-genome shotgun resequencing. It uses a non-greedy algorithm and shows comparable performance and higher accuracy in an evaluation…
The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy,…
New long read sequencing technologies, like PacBio SMRT and Oxford NanoPore, can produce sequencing reads up to 50,000 bp long but with an error rate of at least 15%. Reducing the error rate is necessary for subsequent utilisation of the…
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…
The study of functional genomics--particularly in non-model organisms has been dramatically improved over the last few years by use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
Quantum error correction plays an important role in fault-tolerant quantum information processing. It is usually difficult to experimentally realize quantum error correction, as it requires multiple qubits and quantum gates with high…
Quantum computing devices are inevitably subject to errors. To leverage quantum technologies for computational benefits in practical applications, quantum algorithms and protocols must be implemented reliably under noise and imperfections.…
Near term quantum computers suffer from the presence of different noise sources. In order to mitigate for this effect and acquire results with significantly better accuracy, there is the urge of designing efficient error correction or error…
Due to the fragility of quantum mechanical effects, real quantum computers are plagued by frequent noise effects that cause errors during computations. Quantum error-correcting codes address this problem by providing means to identify and…
Quorum systems are a powerful mechanism for ensuring the consistency of replicated data. Production systems usually opt for majority quorums due to their simplicity and fault tolerance, but majority quorum systems provide poor throughput…
Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…
Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists due to its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina…
k-mers (nucleotide strings of length k) form the basis of several algorithms in computational genomics. In particular, k-mer abundance information in sequence data is useful in read error correction, parameter estimation for genome…
We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol…
Quantum computing has become a promising computing approach because of its capability to solve certain problems, exponentially faster than classical computers. A $n$-qubit quantum system is capable of providing $2^{n}$ computational space…
Quantum error correction is a set of methods to protect quantum information--that is, quantum states--from unwanted environmental interactions (decoherence) and other forms of noise. The information is stored in a quantum error-correcting…
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…