ArticleBioinformatics (Oxford, England)2023
PanKmer: k-mer-based and reference-free pangenome analysis.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 28 citations in OpenAlex.
- Genomic analysis of 3,330 accessions provides insights into the evolutionary history and self-incompatibility locus of the Brassica A genome.Nature genetics · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Persistent trade-offs balance competition and colonization across centuries.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Haploid Mutation Mapping Identifies a Homoeologous Non-Reciprocal Translocation Linked to Reduced Fibre and Enhanced Protein in Brassica napus.Plant biotechnology journal · 2026Article
- Evolutionary and methodological considerations when interpreting gene presence-absence variation in pangenomes.NAR genomics and bioinformatics · 2026Review
- Little millet genome reveals evolutionary insights into tetraploid structure and genetic basis of micronutrient density.Nature communications · 2025Article
- Hybridization and low-light adaptability in California eelgrass (Zostera spp.).Nature plants · 2025Article
- Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes.bioRxiv : the preprint server for biology · 2025Article
- Article
- Jan and mini-Jan, a model system for potato functional genomics.Plant biotechnology journal · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Mem-based pangenome indexing for k-mer queries.Algorithms for molecular biology : AMB · 2025Article
- Can a plant biologist fix a thermostat?The New phytologist · 2025Review
- Comparison of Recombination Rate, Reference Bias, and Unique Pangenomic Haplotypes inInternational journal of molecular sciences · 2025Article
- Complexity welcome: Pangenome graphs for comprehensive population genomics.Quantitative plant biology · 2025Review
- An alignment- and reference-free strategy usingMycology · 2025Article
- Jan and mini-Jan, a model system for potato functional genomics.bioRxiv : the preprint server for biology · 2024Article
- Early Detection of BothInternational journal of molecular sciences · 2024Article
- Multiple Horizontal Mini-chromosome Transfers Drive Genome Evolution of Clonal Blast Fungus Lineages.Molecular biology and evolution · 2024Article
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
summaryPangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome analysis predominantly leverages graph-based methods that require computationally intensive multiple genome alignments, do not scale to highly complex eukaryotic genomes, limit their scope to identifying structural variants (SVs), or incur bias by relying on a reference genome. Here, we present PanKmer, a toolkit designed for reference-free analysis of pangenome datasets consisting of dozens to thousands of individual genomes. PanKmer decomposes a set of input genomes into a table of observed k-mers and their presence-absence values in each genome. These are stored in an efficient k-mer index data format that encodes SNPs, INDELs, and SVs. It also includes functions for downstream analysis of the k-mer index, such as calculating sequence similarity statistics between individuals at whole-genome or local scales. For example, k-mers can be "anchored" in any individual genome to quantify sequence variability or conservation at a specific locus. This facilitates workflows with various biological applications, e.g. identifying cases of hybridization between plant species. PanKmer provides researchers with a valuable and convenient means to explore the full scope of genetic variation in a population, without reference bias. AVAILABILITY AND IMPLEMENTATION: PanKmer is implemented as a Python package with components written in Rust, released under a BSD license. The source code is available from the Python Package Index (PyPI) at https://pypi.org/project/pankmer/ as well as Gitlab at https://gitlab.com/salk-tm/pankmer. Full documentation is available at https://salk-tm.gitlab.io/pankmer/.
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Registered trials
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.