Related papers: RECKONER: Read Error Corrector Based on KMC

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…

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,…

Motivation: Illumina Sequencing data can provide high coverage of a genome by relatively short (100 bp150 bp) reads at a low cost. Our goal is to produce trimmed and error-corrected reads to improve genome assemblies. Our error correction…

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…

Sequencing technologies are prone to errors, making error correction (EC) necessary for downstream applications. EC tools need to be manually configured for optimal performance. We find that the optimal parameters (e.g., k-mer size) are…

A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…

We consider a neural network (NN) that may experience memory faults and computational errors. In this paper, we propose a novel real-number-based error correction code (ECC) capable of detecting and correcting both memory errors and…

Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…

Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often…

Several statistical approaches based on reproducing kernels have been proposed to detect abrupt changes arising in the full distribution of the observations and not only in the mean or variance. Some of these approaches enjoy good…

Current approaches to fault-tolerant quantum computation will not enable useful quantum computation on near-term devices of 50 to 100 qubits. Leading proposals, such as the color code and surface code schemes, must devote a large fraction…

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…

This paper describes a new asynchronous algorithm and implementation for the problem of k-mer counting (KC), which concerns quantifying the frequency of length k substrings in a DNA sequence. This operation is common to many computational…

Quantum computers have the potential to solve certain complex problems in a much more efficient way than classical computers. Nevertheless, current quantum computer implementations are limited by high physical error rates. This issue is…

Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…

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…

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…

In this paper, we present a simple and efficient GEC sequence tagger using a Transformer encoder. Our system is pre-trained on synthetic data and then fine-tuned in two stages: first on errorful corpora, and second on a combination of…

Error correction codes (ECC) are crucial for ensuring reliable information transmission in communication systems. Choukroun & Wolf (2022b) recently introduced the Error Correction Code Transformer (ECCT), which has demonstrated promising…

We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…