Results 11 to 20 of about 57,228 (156)
Mining statistically-solid k-mers for accurate NGS error correction. [PDF]
BMC Genomics, 2018 © 2018 The Author(s). Background: NGS data contains many machine-induced errors. The most advanced methods for the error correction heavily depend on the selection of solid k-mers. A solid k-mer is a k-mer frequently occurring in NGS reads.
Zhao L +8 more
europepmc +2 more sources
Fast Gapped k-mer Counting with Subdivided Multi-Way Bucketed Cuckoo Hash Tables [PDF]
, 2022 Motivation. In biological sequence analysis, alignment-free (also known as k-mer-based) methods are increasingly replacing mapping- and alignment-based methods for various applications.
Rahmann, Sven, Zentgraf, Jens
core +1 more source
The effect of the lateral interactions on the critical behavior of long straight rigid rods on two-dimensional lattices [PDF]
, 2009 Using Monte Carlo simulations and finite-size scaling analysis, the critical behavior of attractive rigid rods of length k (k-mers) on square lattices at intermediate density has been studied.
Linares, D. H. +2 more
core +3 more sources
Alignment-free sequence comparison with spaced k-mers [PDF]
, 2013 Alignment-free methods are increasingly used for genome analysis and phylogeny reconstruction since they circumvent various difficulties of traditional approaches that rely on multiple sequence alignments.
+5 more
core +1 more source
, 2014 K-mer abundance analysis is widely used for many purposes in nucleotide sequence analysis, including data preprocessing for de novo assembly, repeat detection, and sequencing coverage estimation.
Brown, C. Titus +4 more
core +4 more sources
Spaced seeds improve k-mer-based metagenomic classification [PDF]
, 2015 Metagenomics is a powerful approach to study genetic content of environmental samples that has been strongly promoted by NGS technologies. To cope with massive data involved in modern metagenomic projects, recent tools [4, 39] rely on the analysis of k ...
Brinda, Karel +2 more
core +2 more sources
Gerbil: A Fast and Memory-Efficient $k$-mer Counter with GPU-Support [PDF]
, 2016 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.
Erbert, Marius +2 more
core +2 more sources
Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants. [PDF]
, 2019 De novo genetic variants are an important source of causative variation in complex genetic disorders. Many methods for variant discovery rely on mapping reads to a reference genome, detecting numerous inherited variants irrelevant to the phenotype of ...
Brown, C Titus +2 more
core +1 more source
On Weighted k-mer Dictionaries [PDF]
, 2022 We consider the problem of representing a set of k-mers and their abundance counts, or weights, in compressed space so that assessing membership and retrieving the weight of a k-mer is efficient.
Pibiri, Giulio Ermanno
core +3 more sources
Effects of Impurities in Random Sequential Adsorption on a One-Dimensional Substrate
, 1997 We have solved the kinetics of random sequential adsorption of linear $k$-mers on a one-dimensional disordered substrate for the random sequential adsorption initial condition and for the random initial condition. The jamming limits $\theta(\infty, k', k)
A. Réni +11 more
core +2 more sources