ArticleMicrobial genomics2023
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools.
Article in Microbial genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers, 1 of them a synthesis that pooled it.
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Who cites it
56 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.Nature microbiology · 2026Pooled it
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- Comparing the Performance of Double-Stranded and Single-Stranded DNA Libraries for Ancient Oral Microbiome Reconstruction.Molecular ecology resources · 2026Article
- The Biotechnological Applications of Marine Bacteria.Biology · 2026Review
- Metagenomics for antimicrobial resistance: from resistome surveillance to mechanistic inference.Journal of bacteriology · 2026Review
- Ocular community state types reveal distinct microbial compositions among microbiomes with implications for trachoma control.bioRxiv : the preprint server for biology · 2026Article
- Exploring shotgun metagenomic data to detect microeukaryotic pathogens in wildlife.BMC microbiology · 2026Article
- Increased abundance of Limosilactobacillus reuteri in the gut of selectively bred high-tameness mice and its association with behavioural changes.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Comparison of Environmental Microbiomes, Resistomes and Plasmidomes from a Human Tertiary Hospital and Companion Animal Veterinary Hospital in London, UK.Antibiotics (Basel, Switzerland) · 2026Article
- Comparison of short nasal swab and deep nasopharyngeal swab sampling methods to describe BRD-associated viruses and bacteria detected using a metagenomics approach optimized for virus recovery in fall-placed beef calves shortly after feedlot arrival.Veterinary and animal science · 2026Article
- Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.BMC genomics · 2026Article
- TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.Bioinformatics (Oxford, England) · 2026Article
- Kun-peng enables scalable and accurate pan-domain metagenomic classification.Briefings in bioinformatics · 2026Article
- Filtering for truth: high-precision taxonomic classification in nanopore shotgun metagenomics data through a KMA-based bioinformatic pipeline (KAPTAIN).BMC genomics · 2026Article
- Reproducible Emu-Based Workflow for High-Fidelity Soil and Plant Microbiome Profiling on HPC Clusters.Bio-protocol · 2026Article
- PUDU (pipeline for universal diversity unveiling): an accessible end-to-end workflow for taxonomic profiling and ecological visualization of environmental microbiomes across amplicon, shotgun, and long-read sequencing.Frontiers in bioinformatics · 2026Article
- Unlocking the Metagenome: Pipeline for Microbiome Data Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Assessing Amplification Quality and Bias in MDA Methods Through Comparative Analysis of Short-Read Sequencing.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Doing more with less: Genomic quasi-G-primes differentiate septic from healthy patients.PloS one · 2026Article
- Bacterial cell-free DNA profiling reveals the co-elevation of multiple bacteria in newborn foals with suspected sepsis.iScience · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic classification of reads by comparison to a database of previously taxonomically classified genomes. While different studies comparing metagenomic taxonomic classification methods have determined that different tools are 'best', there are two tools that have been used the most to-date: Kraken (
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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.