GigaScience最新文献

{"title":"MIReVTD, a minimum information standard for reporting vector trait data.","authors":"Sadie J Ryan, Paul J Huxley, Catherine A Lippi, Samraat Pawar, Lauren Cator, Samuel S C Rund, Leah R Johnson","doi":"10.1093/gigascience/giag020","DOIUrl":"10.1093/gigascience/giag020","url":null,"abstract":"<p><p>Vector-borne diseases pose a persistent and increasing challenge to human, animal, and agricultural systems globally. Mathematical modeling frameworks incorporating vector trait responses are powerful tools for assessing risk and predicting vector-borne disease impacts. Developing these frameworks and the reliability of their predictions hinge on the availability of experimentally derived vector trait data for model parameterization and inference of the biological mechanisms underpinning transmission. Trait experiments have generated data for many known and potential vector species, but the terminology used across studies is inconsistent, and accompanying publications may share data with insufficient detail for reuse or synthesis. The lack of data standardization can lead to information loss and prohibit analytical comprehensiveness. Here, we present MIReVTD, a Minimum Information standard for Reporting Vector Trait Data. Our reporting checklist balances completeness and labor intensity to make these important experimental data easier to find and reuse, without onerous effort for scientists generating the data. To illustrate the standard, we provide an example reproducing results from an Aedes aegypti mosquito study.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13122843/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147316891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reducing haystacks to needles-ViralClust: a Nextflow pipeline to cluster viral sequences.","authors":"Sandra Triebel, Kevin Lamkiewicz, Tom Eulenfeld, Manja Marz","doi":"10.1093/gigascience/giag090","DOIUrl":"10.1093/gigascience/giag090","url":null,"abstract":"<p><strong>Background: </strong>The rapid accumulation of viral genome sequences presents major challenges for downstream analysis tools, including tools for multiple sequence alignments, phylogeny, and genome/alignment visualization, due to computational constraints and sampling biases caused by outbreak-driven over-representation. Selecting representative genomes through clustering offers a principled alternative to random subsampling, yet choosing appropriate clustering strategies remains non-trivial and context-dependent.</p><p><strong>Results: </strong>Here, we present ViralClust, a modular Nextflow pipeline for bias-aware representative selection from large viral genome datasets. ViralClust integrates 5 distinct clustering algorithms (CD-HIT-EST, SUMACLUST, VSEARCH, MMSeqs2, and HDBSCAN) within a unified workflow, enabling direct comparison of clustering outcomes and flexible adaptation to diverse biological questions, considering a balanced phylogenetic distribution of the selected sequences. We evaluated ViralClust on 6 RNA and DNA virus datasets ranging from 632 to 156,586 sequences and spanning genome lengths from 890 to 197,185 nucleotides. Across all datasets, clustering reduced dataset size by ~95% or more while preserving genetic diversity across species, genera, and families, and effectively mitigating biases introduced by outbreaks, partial genomes, and sequence orientation artifacts.</p><p><strong>Conclusions: </strong>By supporting whole-genome clustering and scalable representative selection, ViralClust enables efficient and reproducible downstream analyses that would otherwise be computationally infeasible. Rather than offering a prescriptive, guided analysis engine, our framework functions as a flexible comparative collection of complementary strategies, allowing users to empirically evaluate trade-offs and choose the ideal method tailored to their specific analytical endpoints.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13660479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148967751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Exploring the role of normalization and feature selection in microbiome disease classification pipelines.","authors":"","doi":"10.1093/gigascience/giag050","DOIUrl":"10.1093/gigascience/giag050","url":null,"abstract":"","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"15 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13148396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147836696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"deMEM: a novel divide-and-conquer framework based on de Bruijn graph for scalable multiple sequence alignment.","authors":"Yanming Wei, Zhaoyang Huang, Pinglu Zhang, Yizheng Wang, Yan Li, Liang Yu, Quan Zou","doi":"10.1093/gigascience/giaf163","DOIUrl":"10.1093/gigascience/giaf163","url":null,"abstract":"<p><strong>Background: </strong>Multiple sequence alignment (MSA) continues to be a central challenge in comparative genomics, where the quality of alignment plays a crucial role in determining the accuracy of downstream analyses. However, the challenge of large-scale alignment remains significant.</p><p><strong>Findings: </strong>This article introduces deMEM, a novel and effective framework for DNA multiple sequence alignment, which enables existing MSA methods such as MAFFT to handle extremely large sequences. deMEM is a 3-stage alignment process: (i) representing maximum exact matches using a de Bruijn graph and clustering them based on their area, (ii) employing a novel divide-and-conquer framework for alignment, and (iii) providing profile-profile alignment between different clusters.</p><p><strong>Conclusions: </strong>DeMEM enables existing methods like MAFFT to align an extremely large number of sequences, including long sequences that cannot be directly aligned, such as those in a dataset of a thousand monkeypox virus genomes. The deMEM package is free and available at https://github.com/malabz/deMEM.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":" ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12878729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145900220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Federated knowledge retrieval elevates large language model performance on biomedical benchmarks.","authors":"Janet Joy, Andrew I Su","doi":"10.1093/gigascience/giag007","DOIUrl":"10.1093/gigascience/giag007","url":null,"abstract":"<p><strong>Background: </strong>Large language models (LLMs) have significantly advanced natural language processing in biomedical research; however, their reliance on implicit, statistical representations often results in factual inaccuracies or hallucinations, posing significant concerns in high-stakes biomedical contexts.</p><p><strong>Results: </strong>To overcome these limitations, we developed BioThings Explorer-Retrieval-Augmented Generation (BTE-RAG), a Retrieval-Augmented Generation framework that integrates the reasoning capabilities of advanced language models with explicit mechanistic evidence sourced from BTE, an API federation of more than sixty authoritative biomedical knowledge sources. We systematically evaluated BTE-RAG in comparison to traditional LLM-only methods across three benchmark datasets that we created from DrugMechDB. These datasets specifically targeted gene-centric mechanisms (798 questions), metabolite effects (201 questions), and drug-biological process relationships (842 questions). On the gene-centric task, BTE-RAG increased accuracy from 51 to 75.8% for GPT-4o mini and from 69.8 to 78.6% for GPT-4o. In metabolite-focused questions, the proportion of responses with cosine similarity scores of at least 0.90 rose by 82% for GPT-4o mini and 77% for GPT-4o. While overall accuracy was consistent in the drug-biological process benchmark, the retrieval method enhanced response concordance, producing a greater than 10% increase in high-agreement answers (from 129 to 144) using GPT-4o. We additionally evaluated BTE-RAG alongside GeneGPT-based models on the GeneTuring gene-disease association benchmark and on our mechanistic gene benchmark, demonstrating that the BTE-RAG layer consistently improves accuracy relative to alternative approaches.</p><p><strong>Conclusion: </strong>Federated knowledge retrieval provides transparent improvements in accuracy for LLMs, establishing BTE-RAG as a valuable and practical tool for mechanistic exploration and translational biomedical research.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12888809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145997110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Experimental and computational approaches for deep metabolome annotation with application to the ecotoxicological model organism Daphnia magna.","authors":"Thomas N Lawson, Martin R Jones, Andrew J Chetwynd, Elena Sostare, Stefan Weidt, Robert Mistrik, Warwick B Dunn, Ralf J M Weber, Mark R Viant","doi":"10.1093/gigascience/giag055","DOIUrl":"10.1093/gigascience/giag055","url":null,"abstract":"<p><strong>Background: </strong>Comprehensively characterizing the metabolomes of model organisms with high coverage and confidence is a critical step towards interpreting the metabolic basis of human and environmental health, yet there are formidable challenges involved in annotating metabolomes. A wide range of genotypes and phenotypes should be sampled with multiple complementary analytical approaches to cover the large and dynamic biochemical space they exhibit. In addition, multiple computational tools and approaches are required to annotate the metabolites from raw analytical data.</p><p><strong>Results: </strong>To address this, we developed the deep metabolome annotation (DMA) workflow. Applied to the ecological sentinel species, Daphnia magna, a pooled sample comprising 10 distinct strains exposed to both normal and stressed environmental conditions was extracted and systematically physicochemically separated via solid-phase extraction and liquid- and gas-chromatography prior to extensive multiple-stage mass spectrometric fragmentation, generating >8,000 raw data files, and supplemented by nuclear magnetic resonance spectroscopy. An extensive Galaxy-based computational approach was built to analyse these data, comprising >30 tools. The overall DMA efforts resulted in 8,181 annotated polar metabolites and lipids in D. magna, with the raw and processed data, tools, and annotations disseminated freely via public data repositories and a custom web-based interface to maximize reusability.</p><p><strong>Conclusions: </strong>The DMA workflow has generated one of the largest metabolome annotation datasets for any non-human model organism and provides the first in-depth characterization of the D. magna metabolome, serving as both a resource and a valuable catalyst for future DMA studies of other model organisms.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13254479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147863873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sex chromosome turnover and structural genome divergence shape meiotic outcomes in hybridizing Cobitis.","authors":"Stephen A Schlebusch, Vladimir Trifonov, Zuzana Halenková, Marharyta Klianitskaya, Dmitrij Dedukh, Aurora Ruiz-Herrera, Lucia Álvarez-González, Gala Pujol, Eva Hřibová, Lucija Andjel, Oldřich Bartoš, Petr Pajer, Tomáš Tichopád, Daniel Kulik, Jan Kotusz, Marie Kaštánková Doležálková, Astrid Böhne, Anatolie Marta, Patrik Horna, Radka Reifová, Yann Guiguen, Heiner Kuhl, Jan Pačes, Karel Janko","doi":"10.1093/gigascience/giag031","DOIUrl":"10.1093/gigascience/giag031","url":null,"abstract":"<p><strong>Background: </strong>Hybridization between divergent species can result in meiotic aberrations and the emergence of asexual reproduction. Yet, it remains poorly understood to what extent such outcomes arise from genome-wide incompatibilities versus more specific conflicts among individual chromosomes inherited from parental species, including their ability to pair during meiosis in hybrids. It is also unclear how interspecific hybrids cope with differences in sex determination systems, particularly in the context of increased ploidy. Addressing these questions requires high-quality, chromosome-level reference genomes of the parental species involved in hybrid formation.</p><p><strong>Findings: </strong>Here, we present the first chromosome-level genome assemblies for three hybridizing Cobitis species (C. elongatoides, C. taenia, and C. tanaitica), providing a comprehensive framework for investigating the genomic and cytogenetic basis of hybrid sterility and the transition to asexuality. By integrating genome scaffolding, male/female pooled sequencing (Pool-Seq), and molecular cytogenetics, we uncover extensive structural variation among homologous chromosomes of the three species, despite overall karyotype conservation. Population-level analyses revealed that each species possesses distinct, non-homologous sex chromosomes, highlighting rapid sex chromosome turnover in this recently diverged lineage. Finally, the design of chromosome-specific painting probes, which we applied to meiotic metaphase I spreads of diploid hybrids. This approach revealed striking differences in the pairing success of orthologous chromosomes.</p><p><strong>Conclusions: </strong>Our results demonstrate that individual orthologous chromosomes differ markedly in their ability to form bivalents during meiosis in hybrids, indicating that hybrid meiotic behaviour is shaped by chromosome-specific incompatibilities rather than uniform genome-wide failure. We also found that even closely related parental species possess distinct, non-homologous sex chromosomes, highlighting rapid turnover of sex determination systems in hybridizing lineages. Together, these findings provide a high-resolution genomic and cytogenetic framework to explore how the architecture of inherited parental genomes influences sex-specific reproductive outcomes in hybrids-ranging from male sterility to the establishment of fertile, clonally reproducing female lineages-and how such asymmetries may contribute to the emergence of asexuality in vertebrates.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13175044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147503572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Draft assemblies for 177 bird species enhance genus-level coverage.","authors":"Guangji Chen, Shuang Wang, Daniel Bilyeli Øksnebjerg, Sascha Dreyer Nielsen, Wei Dai, Wei Jiang, Jing Liang, Wei Han, Chengran Zhou, Qiye Li, Bent Petersen, Ara Monadjem, Zamekile D Bhembe, Machawe Maphalala, Diego Ocampo, Luis Sandoval, Jörns Fickel, Alex D Greenwood, Claudia A Szentiks, Marco Roller, Sharon M Birks, Adam D Leaché, Alejandro Rico-Guevara, Jérôme Fuchs, Nguyen Tran Vy, Christina Hvilsom, Juliana Andrea Berner, Jan Terje Lifjeld, Arild Johnsen, Lars Erik Johannessen, Kim Labuschagne, Knud Andreas Jønsson, Martin Irestedt, Andrew Hart Reeve, Leo Joseph, Olof Hellgren, Robb T Brumfield, Theresa M Burg, Juan Carlos Illera, Alexandre Aleixo, Ben Smit, Frank E Rheindt, Jessica Lee, Isao Nishiumi, Javier Quesada, John P Dumbacher, Manuel Schweizer, Michael J Andersen, Christopher C Witt, Richard A Phillips, Richard O Prum, Kristof Zyskowski, Steven M Goodman, Marie Jeanne Raherilalao, Ulf Ottosson, Yahkat Barshep, Sam Ivande, Vojtěch Brlík, Emmanuel Okposio, Bonny Koane, Tri Haryoko, Erich D Jarvis, Carsten Rahbek, Fumin Lei, Gary R Graves, Shaohong Feng, Peter A Hosner, M Thomas P Gilbert, Guojie Zhang","doi":"10.1093/gigascience/giag045","DOIUrl":"10.1093/gigascience/giag045","url":null,"abstract":"<p><strong>Background: </strong>With over 10,000 recognized species, birds constitute one of the most diverse and widely distributed vertebrate groups. Although avian genomics has advanced rapidly over the past decade, substantial gaps remain across the global avifauna. Filling these gaps is essential for understanding macroevolutionary patterns, population structure, and the molecular basis of ecological and behavioral diversity. Worldwide museum collections represent invaluable resources for filling these gaps, yet the typically degraded DNA and limited quantities from historical specimens have posed significant challenges for generating high-quality genome assemblies.</p><p><strong>Results: </strong>Here, the Bird Genome 10 K Project adopted low-input sequencing strategies that reduce costs while improving assembly quality compared with earlier order- and family-level genomes. Using mainly stLFR, complemented by 10X Genomics and standard next-generation sequencing, we assembled 177 avian genomes from museum specimens and tissue collections representing 161 genera, including 102 newly sequenced at the genomic level. The assemblies average ∼1.2 Gb in size, with scaffold N50 = 8.03 Mb, contig N50 = 120 kb, 93% BUSCO completeness, and Merqury Quality Value score of 56.</p><p><strong>Conclusions: </strong>These genomes greatly expand avian taxonomic coverage and demonstrate the efficiency of low-input sequencing for generating high-quality assemblies from limited and often degraded material sourced from museum specimens. This resource provides a foundation for comparative genomics, conservation genetics, and evolutionary studies across the avian tree of life.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13274736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147863897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analysis of 163 ant genomes reveals recurrent horizontal gene transfer from bacteria to ants.","authors":"Janina L Rinke, Lukas Franke, Ding He, Maike L Fischer, Joel Vizueta, Lars A Eicholt, Rasmus S Larsen, Zijun Xiong, Phoebe Cunningham, Lee M Henry, Martin Kaltenpoth, Jürgen Gadau, Guojie Zhang, Jacobus J Boomsma, Lukas Schrader","doi":"10.1093/gigascience/giag043","DOIUrl":"10.1093/gigascience/giag043","url":null,"abstract":"<p><strong>Background: </strong>Horizontal gene transfer (HGT) from bacteria can drive phenotypic innovation and adaptation in eukaryotes. Ants are likely carriers of HGT-derived genes, as they have repeatedly established mutualistic associations with vertically transmitted bacterial symbionts with direct access to the germline. However, the prevalence of HGT across ants and most other insects remains virtually unexplored.</p><p><strong>Results: </strong>Here, we systematically investigated the genomes of over 160 species of ants and uncovered 497 protein-coding HGT events in 85 species, predominantly derived from intracellular symbionts. Among these, we identified several HGTs likely underpinning functional innovations, primarily by mediating immune-system adaptations or facilitating nutritional niche expansions. Several of these HGTs were conserved in sequence and synteny across multiple species, consistent with strong signatures of purifying selection over up to 40 million years. Functional and structural analysis of a horizontally acquired Xanthine-guanine phosphoribosyltransferase gene of Cardiocondyla ants reveals deep entrenchment of this protein in basic energy metabolism of the host, facilitated by the enzyme's substrate promiscuity.</p><p><strong>Conclusions: </strong>This study provides insights into the abundance and diversity of HGT from bacteria in the evolutionary history of ants. Furthermore, our comparative and functional analyses suggest that many of the horizontally acquired genes serve adaptive functions in ants, most prominently by expanding metabolic pathways or modulating immune responses.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13320244/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147633260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CamK-DB: A k-mer MinHash fingerprint database for reference-free genotyping of Camellia accessions.","authors":"Feiquan Wang, Noor-Ul Áin, Fang Wang, Shengcheng Zhang, Weilong Kong, Yutao Shi, Hua Feng, Bo Zhang, Xingtan Zhang","doi":"10.1093/gigascience/giag088","DOIUrl":"10.1093/gigascience/giag088","url":null,"abstract":"<p><p>Tea (Camellia sinensis L.), a major global economic crop in Asia, poses challenges for genetic identification because its highly heterozygous, repetitive genome reduces the efficacy of conventional single-nucleotide polymorphism (SNP) and microsatellite markers, and interspecific hybridization further complicates the situation. To address these issues, CamK-DB was developed as a reference-free Camellia fingerprinting database built on MIKE MinHash sketches. We curated 418 candidate resequencing datasets, and built a database using standardized 5× genome-coverage fingerprints. Each accession is stored as a MIKE. jac fingerprint generated with k = 21 and recommended sketch/pre_cnt = 2000. CamK-DB provides a command-line interface for data management and a custom C++ query engine that computes top-10 matches using Jaccard similarity, complemented by a QT-based graphical interface for interactive analysis. This resource offers a robust and scalable framework for precise and routine germplasm identification, genomic phylogenetic inference, and strategic breeding program design. CamK-DB (database and code) is publicly available at https://github.com/sc-zhang/CamK-DB. CamK-DB binaries are provided for Windows 10/11 and Linux (x86_64, glibc ≥ 2.27).</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13548848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148791698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}