ArticlePLoS computational biology2017
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 52 citations in OpenAlex.
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Local Genomic Surveillance of InvasiveInternational journal of molecular sciences · 2024Article
- Whole genome sequencing of human Borrelia burgdorferi isolates reveals linked blocks of accessory genome elements located on plasmids and associated with human dissemination.PLoS pathogens · 2023Article
- Whole genome sequencing ofbioRxiv : the preprint server for biology · 2023Article
- Comparison of k-mer-basedMicrobiome research reports · 2023Article
- The first long-read nuclear genome assembly of Oryza australiensis, a wild rice from northern Australia.Scientific reports · 2022Article
- AutoCoV: tracking the early spread of COVID-19 in terms of the spatial and temporal patterns from embedding space by K-mer based deep learning.BMC bioinformatics · 2022Article
- Feature extraction based on microstate sequences for EEG-based emotion recognition.Frontiers in psychology · 2022Article
- EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.NAR genomics and bioinformatics · 2021Article
- Estimating Genetic Similarity Matrices Using Phylogenies.Journal of computational biology : a journal of computational molecular cell biology · 2021Article
- Article
- An Information-Entropy Position-WeightedFrontiers in genetics · 2021Article
- A Computational Framework for Pattern Detection on Unaligned Sequences: An Application on SARS-CoV-2 Data.Frontiers in genetics · 2021Article
- Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci.PLoS genetics · 2020Article
- Information Theory in Computational Biology: Where We Stand Today.Entropy (Basel, Switzerland) · 2020Article
- To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics.Nucleic acids research · 2020Article
- Positional Correlation Natural Vector: A Novel Method for Genome Comparison.International journal of molecular sciences · 2020Article
- Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels.Genome biology and evolution · 2020Article
- Integrated Genome-Wide Analysis of an Isogenic Pair ofInternational journal of molecular sciences · 2020Article
- The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances.PloS one · 2020Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or "samples") in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include establishing sample identity and detecting mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.