Related papers: Extraction of long k-mers using spaced seeds

For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots…

Sequence segmentation is a well-studied problem, where given a sequence of elements, an integer K, and some measure of homogeneity, the task is to split the sequence into K contiguous segments that are maximally homogeneous. A classic…

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…

Large language models (LLMs) are increasingly touted as powerful tools for automating scientific information extraction. However, existing methods and tools often struggle with the realities of scientific literature: long-context documents,…

In this article, we review existing probabilistic models for modeling abundance of fixed-length strings (k-mers) in DNA sequencing data. These models capture dependence of the abundance on various phenomena, such as the size and repeat…

Enormous volumes of short reads data from next-generation sequencing (NGS) technologies have posed new challenges to the area of genomic sequence comparison. The multiple sequence alignment approach is hardly applicable to NGS data due to…

Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…

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…

Sequence classification has numerous applications in various fields. Despite extensive studies in the last decades, many challenges still exist, particularly in pattern-based methods. Existing pattern-based methods measure the…

Motivation: RNA-seq has made feasible the analysis of a whole set of expressed mRNAs. Mapping-based assembly of RNA-seq reads sometimes is infeasible due to lack of high-quality references. However, de novo assembly is very challenging due…

This paper provides a comprehensive review of recent advancements in k-mer-based data structures representing collections of several samples (sometimes called colored de Bruijn graphs) and their applications in large-scale sequence indexing…

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…

A basic task in bioinformatics is the counting of $k$-mers in genome strings. The $k$-mer counting problem is to build a histogram of all substrings of length $k$ in a given genome sequence. We present the open source $k$-mer counting…

We propose a frame-based representation of k-mers for detecting sequencing errors and rare variants in next generation sequencing data obtained from populations of closely related genomes. Frames are sets of non-orthogonal basis functions,…

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower…

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…

Brown et al.\ (2025) described a pre-processing step, called $k$-mer based breaking (KeBaB), that speeds up searching for long maximal exact matches (MEMs) between a pattern $P$ and an indexed repetitive text $T$. KeBaB produces a set of…

RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…

Modern high throughput sequencing technologies like metagenomic sequencing generate millions of sequences which have to be classified based on their taxonomic rank. Modern approaches either apply local alignment and comparison to existing…

Motivated by the increasing availability of low- and mixed-precision arithmetic on modern hardware, we develop mixed-precision variants of Lloyd's algorithm for k-means clustering. The main ingredient is a family of mixed-precision kernels…