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Metagenome analysis using the Kraken software suite

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Rapid and sensitive detection of genome contamination at scale with FCS-GX

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The complete sequence of a human Y chromosome

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GUNC: detection of chimerism and contamination in prokaryotic genomes

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Major data analysis errors invalidate cancer microbiome findings

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A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas

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HGT is widespread in insects and contributes to male courtship in lepidopterans

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Plant pan-genomics and its applications

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Unifying the known and unknown microbial coding sequence space

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ElasticBLAST: accelerating sequence search via cloud computing

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Unlocking the potential of marine biodiscovery

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Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data

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SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes

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Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century

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Examples of Extreme Survival: Tardigrade Genomics and Molecular Anhydrobiology

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How clear is our current view on microbial dark matter? (Re-)assessing public MAG & SAG datasets with MDMcleaner

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Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts

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UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi

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Sharp Increase of Problematic Mitogenomes of Birds: Causes, Consequences, and Remedies

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Simplitigs as an efficient and scalable representation of de Bruijn graphs

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Pleistocene glacial and interglacial ecosystems inferred from ancient DNA analyses of permafrost sediments from Batagay megaslump, East Siberia

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Long‐ and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities

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The role of microbiome-host interactions in the development of Alzheimer´s disease

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A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling

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De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee

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Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics

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ngs LCA —A toolkit for fast and flexible lowest common ancestor inference and taxonomic profiling of metagenomic data

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The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modelingPreprint

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The spatiotemporal distribution of human pathogens in ancient Eurasia

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Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus

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An 8000 years old genome reveals the Neolithic origin of the zoonosis Brucella melitensis

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The NIH Comparative Genomics Resource: addressing the promises and challenges of comparative genomics on human health

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ATP binding cassette importers in eukaryotic organisms

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An automated workflow to assess completeness and curate GenBank for environmental DNA metabarcoding: The marine fish assemblage as case study

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Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade

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Propagation, detection and correction of errors using the sequence database network

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Environmental DNA metabarcoding of cow dung reveals taxonomic and functional diversity of invertebrate assemblages

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High incidence of mislabeling and a hint of fraud in the ceviche and sushi business

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Detection and monitoring of insect traces in bioaerosols

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Minimally overlapping words for sequence similarity search

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Building genomic infrastructure: Sequencing platinum‐standard reference‐quality genomes of all cetacean species

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Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data

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Global controversy in oyster systematics and a newly described species from SE Asia (Bivalvia: Ostreidae: Crassostreinae)

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Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits

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GUNC: Detection of Chimerism and Contamination in Prokaryotic GenomesPreprint

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The new microbiome on the block: challenges and opportunities of using human tumor sequencing data to study microbes

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Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity

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Enhanced Arbovirus Surveillance with High-Throughput Metatranscriptomic Processing of Field-Collected Mosquitoes

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Pan-genome analysis reveals genomic variations during enoki mushroom domestication, with emphasis on genetic signatures of cap color and stipe length

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Protein Structural Phylogenetics

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CONSULT: accurate contamination removal using locality-sensitive hashing

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ContScout: sensitive detection and removal of contamination from annotated genomes

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Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective

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Exploring the potential of dental calculus to shed light on past human migrations in Oceania

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Bronze Age Yersinia pestis genome from sheep sheds light on hosts and evolution of a prehistoric plague lineage

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Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies

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Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes

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Comparison of the Efficiency of Single-Locus Species Delimitation Methods: A Case Study of a Single Lake Fish Population in Comparison against the Barcodes from International Databases

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A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples

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Elimination of Foreign Sequences in Eukaryotic Viral Reference Genomes Improves the Accuracy of Virome Analysis

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Diagnostic Stewardship for Next-Generation Sequencing Assays in Clinical Microbiology

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Potential plant extinctions with the loss of the Pleistocene mammoth steppe

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Future Applications of Metagenomic Next-Generation Sequencing for Infectious Diseases Diagnostics

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Advanced prokaryotic systematics: the modern face of an ancient science

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Reliable detection of Host-Microbe Signatures in cancer using PRISM

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The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data

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An Adagio for Viruses, Played Out on Ancient DNA

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Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events

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A High-Throughput Short Sequence Typing Scheme for Serratia marcescens Pure Culture and Environmental DNA

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Post‐transfer adaptation of HGT ‐acquired genes and contribution to guanine metabolic diversification in land plants

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The Situation of Counterfeited and Mislabeled Commercialized Edible Mushrooms in China and the Development of Possible Controls

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Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818)

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Unifying the known and unknown microbial coding sequence spacePreprint

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Mabs, a suite of tools for gene-informed genome assembly

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Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens

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Bird genetic databases need improved curation and error reporting to NCBI

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Simultaneous microbial electrochemical degradation of methyl orange and bioelectricity generation using coculture as anode inoculum in a microbial fuel cell

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Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host

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Enhanced Symbiotic Characteristics in Bacterial Genomes with the Disruption of rRNA Operon

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De novo genome assembly and genome skims reveal LTRs dominate the genome of a limestone endemic Mountainsnail (Oreohelix idahoensis)

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Feasibility of applying shotgun metagenomic analyses to grapevine leaf, rhizosphere and soil microbiome characterisation

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Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification

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iGDP : An integrated genome decontamination pipeline for wild ciliated microeukaryotes

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Nanopore Sequencing Data Analysis of 16S rRNA Genes Using the GenomeSync-GSTK System

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Biological databases in the age of generative artificial intelligence

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Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes

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Targeted decontamination of sequencing data with CLEAN

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Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing

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Contamination in Reference Sequence Databases: Time for Divide-and-Rule Tactics

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Contamination in sequence databases

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Additional file 3 of Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

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Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies

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acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data

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