ArticleBMC genomics2015
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 305 papers, 3 of them syntheses that pooled it.
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305 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Computational paradigms for antimicrobial resistance prediction: integrating multi-omics, structural modeling, and foundation artificial intelligence systems.Briefings in bioinformatics · 2026Pooled it
- Bioinformatics Tools and Approaches for Virus Discovery in Genomic Data: A Systematic Review.Viruses · 2025Pooled it
- Gut Bacteroides act in a microbial consortium to cause susceptibility to severe malaria.Nature communications · 2023Pooled it
- Dance and Dietary Intervention Improves Metabolic Health, Fitness, and Quality of Life With Modest Gut Microbiota Shifts in Breast Cancer Patients With Obesity: A Pilot RCT.Cancer reports (Hoboken, N.J.) · 2026Trial
- Nanopore Sequencing for Chikungunya Virus: Principles and Application.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.Briefings in bioinformatics · 2026Article
- TDKC (Target Distilled K-mer Classifier): Ultrafast and Memory-Efficient Sequence Classification for Target Pathogen Diagnostics.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.BMC genomics · 2026Article
- FALCON2: compression-based metagenomic classification of ancient viruses.Bioinformatics (Oxford, England) · 2026Article
- Efficient and interpretable DNA/RNA representation using Komlós-Hadamard transforms.BMC bioinformatics · 2026Article
- Strain-level metagenomic profiling using pangenome graphs with PanTax.Genome research · 2026Article
- HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.GigaScience · 2026Article
- MADRe: Strain-level metagenomic classification through assembly-driven database reduction.GigaScience · 2026Article
- DeepTaxa: a hybrid CNN-BERT framework for 16S rRNA taxonomic classification.Bioinformatics advances · 2026Article
- Distinct effects of a dairy probiotic drink and physical exercise on gut microbiota in pediatric acute lymphoblastic leukemia patients in remission: a randomized clinical trial.Frontiers in microbiology · 2026Article
- Refining filtering criteria of Kraken family of tools for accurate taxonomic profiling of ancient metagenomic data.Frontiers in microbiology · 2026Article
- A foundational quantum framework for multi-pattern string matching in k-mer detection.Frontiers in bioinformatics · 2026Article
- Reference-free k-mer based dissimilarity measures for metagenomes comparison.Frontiers in bioinformatics · 2026Article
- A correlation analysis between arsenic and mercury resistance and the spread of antibiotic resistance genes in bacteria isolated from a highly contaminated brownfield.Frontiers in microbiology · 2026Article
- Quantum implementation of multi-pattern string matching for k-mer detection.bioRxiv : the preprint server for biology · 2025Article
245 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
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Abstract
backgroundThe problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively studied, it is still computationally challenging due to size of the datasets that modern sequencing technologies can produce.
resultsWe introduce CLARK a novel approach to classify metagenomic reads at the species or genus level with high accuracy and high speed. Extensive experimental results on various metagenomic samples show that the classification accuracy of CLARK is better or comparable to the best state-of-the-art tools and it is significantly faster than any of its competitors. In its fastest single-threaded mode CLARK classifies, with high accuracy, about 32 million metagenomic short reads per minute. CLARK can also classify BAC clones or transcripts to chromosome arms and centromeric regions.
conclusionsCLARK is a versatile, fast and accurate sequence classification method, especially useful for metagenomics and genomics applications. It is freely available at http://clark.cs.ucr.edu/ .
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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.