ArticleGenome biology2018
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 300 papers.
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Who cites it
300 citing papers in PubMed.
- Tumor ecosystem and microbiome features associated with efficacy and resistance to avelumab plus chemoradiotherapy in head and neck cancer.Nature cancer · 2026Trial
- Trial
- Perseus: lineage-aware refinement of Kraken2 taxonomic classification for long read metagenomes.Bioinformatics (Oxford, England) · 2026Article
- Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.Molecular ecology resources · 2026Article
- Improving Metagenomics Classification with Kmask: Entropy-Based Masking of Low-Complexity Regions.bioRxiv : the preprint server for biology · 2026Article
- A refined phylochronology of the second plague pandemic in Western Eurasia.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Three thousand five hundred years of sheeppox virus evolution inferred from archaeological and codicological genomes.Science advances · 2026Article
- Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.Briefings in bioinformatics · 2026Article
- Evidence of dengue transmission and a diverse Aedes mosquito virome on the Congo's Angola border.Nature communications · 2026Article
- TDKC (Target Distilled K-mer Classifier): Ultrafast and Memory-Efficient Sequence Classification for Target Pathogen Diagnostics.bioRxiv : the preprint server for biology · 2026Article
- Brain Transcriptomic Reprogramming and Comb-Associated Microbiome Variation During the Larva-To-Pupa Transition in Apis Mellifera.Archives of insect biochemistry and physiology · 2026Article
- Salt/alkali‑tolerant Streptomyces luteus TRM 45540 improves pepper growth and soil quality in acidic and alkaline soils.BMC plant biology · 2026Article
- RNA in Plasma Extracellular Vesicles of Adolescent Rhesus Macaques Reveals Immune, Bioenergetic, and Microbial Imprints of Early-Life Adversity: An Exploratory Analysis.Biological psychiatry · 2026Article
- Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body.Nature biotechnology · 2026Article
- Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.mSphere · 2026Article
- Investigating ancient human DNA preservation on cave walls and in rock art.Nature communications · 2026Article
- Genestrip: exact and efficient read classification for selected groups of organisms.BMC bioinformatics · 2026Article
- Pathogen detection in central nervous system infections: moving metagenomic sequencing closer to clinical practice.BMC infectious diseases · 2026Article
- Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years.Nature communications · 2026Article
- Evidence of sheeppox in seventeenth-to nineteenth-century France: a multi-disciplinary investigation of a sheep mass mortality assemblage.Royal Society open science · 2026Article
240 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
False-positive identifications are a significant problem in metagenomics classification. We present KrakenUniq, a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory. KrakenUniq is freely available at https://github.com/fbreitwieser/krakenuniq .
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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.