ArticleGenome biology2019
Skmer: assembly-free and alignment-free sample identification using genome skims.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed.
- Plant species identification by genome skimming across the vascular plant tree of life.The New phytologist · 2026Article
- Estimation of substitution and indel rates via k-mer statistics.Algorithms for molecular biology : AMB · 2026Article
- A k-mer-based estimator of the substitution rate between repetitive sequences.Algorithms for molecular biology : AMB · 2026Article
- The gift of novelty: repeat-robust k-mer-based estimators of mutation rates.Bioinformatics (Oxford, England) · 2026Article
- DipSkmer: Reference-free population genomics with diploid genome skims.bioRxiv : the preprint server for biology · 2026Article
- ReSkmer: modeling repeats allows k-mer-based alignment-free methods to calculate population genomic distances.Genome biology · 2026Article
- DNA barcodes analyses provide insights into species delineation and possible cryptic species in Amentotaxus (Taxaceae).BMC plant biology · 2026Article
- The gift of novelty: repeat-robustbioRxiv : the preprint server for biology · 2026Article
- WASTER: Practical de novo Phylogenomics from Low-coverage Short Reads.Molecular biology and evolution · 2026Article
- DNA-based identification of plants and the genomic nature of plant species differences.Communications biology · 2026Article
- Beyond the core microbiome: endemic bacteria drive functional and microdiversity differences across salamander populations.ISME communications · 2026Article
- MeTAline: enabling reproducible and scalable metagenomic analyses.NAR genomics and bioinformatics · 2025Article
- MELO-ED: learning locality-sensitive multi-embeddings for edit distance.bioRxiv : the preprint server for biology · 2025Article
- High species discrimination inPlant diversity · 2025Article
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
- Estimation of substitution and indel rates viaAlgorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- A composite universal DNA signature for the tree of life.Nature ecology & evolution · 2025Article
- Rapid species-level metagenome profiling and containment estimation with sylph.Nature biotechnology · 2025Article
- Inter-Island Whole-Genome Comparison Reveals Micro-Evolutionary Dynamics of the Red Fox, Stimulated Through Post-Glacial Sea-Level Alterations.Genome biology and evolution · 2025Article
- Estimation of substitution and indel rates viabioRxiv : the preprint server for biology · 2025Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data. In contrast, we suggest using all unassembled reads. We introduce an assembly-free and alignment-free tool, Skmer, to compute genomic distances between the query and reference genome skims. Skmer shows excellent accuracy in estimating distances and identifying the closest match in reference datasets.
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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.