ReviewFrontiers in bioinformatics2024
Ten common issues with reference sequence databases and how to mitigate them.
Review in Frontiers in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
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- Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.Nature biotechnology · 2026Article
- Ocular community state types reveal distinct microbial compositions among microbiomes with implications for trachoma control.bioRxiv : the preprint server for biology · 2026Article
- Genome assemblies and annotations are not static and need support for tracking their evolution.Briefings in bioinformatics · 2026Review
- To Beet or Not (Just) to Beet: Ecology, Virulence and Genomic Insights Into the Leaf Spot Disease Causative Pseudomonas syringae pv. aptata.Molecular plant pathology · 2026Review
- Spatial Complexity and Rare-Taxon Turnover Structures Benthic Coral Reef eDNA Communities.Molecular ecology · 2026Article
- ProbeST: a custom probe design pipeline for dual host-pathogen Spatial Transcriptomics.BMC genomics · 2026Article
- Leakage-Safe ITS1 Identification of Fasciola hepatica and Fasciola gigantica with Reverse-Complement-Invariant CNN Inference.Acta parasitologica · 2026Article
- Sedimentary Metagenomics Reveal Avian Community Transitions From the Last Glacial Maximum to the Holocene.Ecology and evolution · 2026Article
- Two novel real-time PCR assays forMicrobiology spectrum · 2026Article
- Genomic insights intoMicrobiology spectrum · 2026Article
- A genomic approach for accurate identification of closely related species with next-generation sequencing samples.Scientific reports · 2026Article
- From Permits to Samples: Addressing Key Challenges for High-Quality Reference Genome Generation in Europe.Molecular ecology resources · 2026Review
- Article
- A framework of Microbial Genomic Database for clinical metagenomic pathogen diagnosis: development and multi-cohort evaluation.Frontiers in cellular and infection microbiology · 2026Article
- The evolution of diagnostic microbiology: integrating culture-based methods and genomic advances.PeerJ · 2026Review
- How low can you go? Establishing detection limits for rare eukaryotes in Southern Ocean sedimentary ancient DNA.Bioinformatics advances · 2026Article
- Decoding the power of the microbiome in human health.Frontiers in cellular and infection microbiology · 2026Review
- RefSeq-corrected transcriptomic and RNA-interaction integration maps medium-associated vancomycin response rewiring inFrontiers in microbiology · 2026Article
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Abstract
Metagenomic sequencing has revolutionized our understanding of microbiology. While metagenomic tools and approaches have been extensively evaluated and benchmarked, far less attention has been given to the reference sequence database used in metagenomic classification. Issues with reference sequence databases are pervasive. Database contamination is the most recognized issue in the literature; however, it remains relatively unmitigated in most analyses. Other common issues with reference sequence databases include taxonomic errors, inappropriate inclusion and exclusion criteria, and sequence content errors. This review covers ten common issues with reference sequence databases and the potential downstream consequences of these issues. Mitigation measures are discussed for each issue, including bioinformatic tools and database curation strategies. Together, these strategies present a path towards more accurate, reproducible and translatable metagenomic sequencing.
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