ArticleBioinformatics (Oxford, England)2013
Scalable metagenomic taxonomy classification using a reference genome database.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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Who cites it
112 citing papers in PubMed.
- 16S rRNA sequence captures microbial functional potential.bioRxiv : the preprint server for biology · 2026Article
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- Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification.mSystems · 2025Article
- Efficient and robust search of microbial genomes via phylogenetic compression.Nature methods · 2025Article
- Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2.aBIOTECH · 2024Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Long journey of 16S rRNA-amplicon sequencing toward cell-based functional bacterial microbiota characterization.iMetaOmics · 2024Review
- Comparative transcriptomic analysis of Staphylococcus epidermidis associated with periprosthetic joint infection under in vivo and in vitro conditions.International journal of medical microbiology : IJMM · 2024Article
- Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases.Veterinary sciences · 2024Review
- Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data.Genome biology and evolution · 2024Article
- CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing.Bioinformatics (Oxford, England) · 2024Article
- Novel Techniques and Models for Studying the Role of the Gut Microbiota in Drug Metabolism.European journal of drug metabolism and pharmacokinetics · 2024Review
- Intravenous ferric carboxymaltose and ferric derisomaltose alter the intestinal microbiome in female iron-deficient anemic mice.Bioscience reports · 2023Article
- StrainIQ: A NovelGenes · 2023Article
- Matchtigs: minimum plain text representation of k-mer sets.Genome biology · 2023Article
- A convenient correspondence between k-mer-based metagenomic distances and phylogenetically-informed β-diversity measures.PLoS computational biology · 2023Article
- Gut microbiota modulates bleomycin-induced acute lung injury response in mice.Respiratory research · 2022Article
- Comparison between Symptomatic and Asymptomatic Mice afterMicroorganisms · 2022Article
- Strain level microbial detection and quantification with applications to single cell metagenomics.Nature communications · 2022Article
52 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationDeep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge.
resultsA method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take <20 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample. AVAILABILITY: Software was implemented in C++ and is freely available at http://sourceforge.net/projects/lmat CONTACT: allen99@llnl.gov SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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