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References from Data mining of public genomic repositories: harnessing off-target reads to expand microbial pathogen genomic resources. Local targets link to admitted publications; unresolved targets remain external evidence.
Basic local alignment search tool
10.1016/s0022-2836(05)80360-2 · 1990 · External reference
Predicting novel mosquito-associated viruses from metatranscriptomic dark matter
10.1093/nargab/lqae077 · 2024 · External reference
Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions
10.1186/s12915-017-0366-6 · 2017 · External reference
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
10.1089/cmb.2012.0021 · 2012 · External reference
The global spread of crop pests and pathogens
10.1111/geb.12214 · 2014 · External reference
Trimmomatic: a flexible trimmer for Illumina sequence data
10.1093/bioinformatics/btu170 · 2014 · External reference
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
10.1371/journal.pcbi.1006650 · 2019 · External reference
The hidden life of Xylella: Mining the NCBI Sequence Read Archive reveals potential new species, host plants and infected areas for this elusive bacterial plant pathogen
10.1101/2025.04.18.649540 · 2025 · External reference
Unresolved reference
2014 · External reference
fastp: an ultra-fast all-in-one FASTQ preprocessor
10.1093/bioinformatics/bty560 · 2018 · External reference
Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity
10.1101/2024.07.30.605881 · 2024 · External reference
Insights into the RNA Virome of the Corn Leafhopper Dalbulus maidis, a Major Emergent Threat of Maize in Latin America
10.3390/v16101583 · 2024 · External reference
Petabase-scale sequence alignment catalyses viral discovery
10.1038/s41586-021-04332-2 · 2022 · External reference
Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations
10.1016/j.tim.2018.11.003 · 2019 · External reference
MultiQC: summarize analysis results for multiple tools and samples in a single report
10.1093/bioinformatics/btw354 · 2016 · External reference
Characterization of the Virome Associated with the Ubiquitous Two-Spotted Spider Mite, Tetranychus urticae.
10.3390/v16101532 · 2024 · External reference
Reconstructing Prehistoric Viral Genomes from Neanderthal Sequencing Data
10.3390/v16060856 · 2024 · External reference
Haplotype-based variant detection from short-read sequencing
10.48550/arxiv.1207.3907 · 2012 · External reference
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii
10.1093/ve/veae040 · 2024 · External reference
Metadata retrieval from sequence databases with ffq
10.1093/bioinformatics/btac667 · 2023 · External reference
Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains
10.1038/s41467-023-41174-0 · 2023 · External reference
Using artificial intelligence to document the hidden RNA virosphere
10.1016/j.cell.2024.09.027 · 2024 · External reference
Recovering ecological interactions by mining non-target data from whole genome re-sequencing projects
10.1101/2025.01.17.633498 · 2025 · External reference
Hidden Viral Sequences in Public Sequencing Data and Warning for Future Emerging Diseases
10.1128/mbio.01638-21 · 2021 · External reference
Entrez Direct: E-utilities on the Unix Command Line
2013 · External reference
Indexing All Life’s Known Biological Sequences
10.1101/2020.10.01.322164 · 2024 · External reference
STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions
10.1186/s13059-021-02490-0 · 2021 · External reference
Hidden Viral Sequences in Public Sequencing Data and Warning for Future Emerging Diseases
10.1128/mbio.01638-21 · 2021 · External reference
Large-scale investigation of zoonotic viruses in the era of high-throughput sequencing
10.1111/1348-0421.13033 · 2023 · External reference
Assembly of long, error-prone reads using repeat graphs
10.1038/s41587-019-0072-8 · 2019 · External reference
Diversity and evolution of viroids and viroid-like agents with circular RNA genomes revealed by metatranscriptome mining
10.1093/nar/gkae1278 · 2025 · External reference
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
10.1093/bioinformatics/btz305 · 2019 · External reference
Genetic variations and gene expression profiles of Rice Black-streaked dwarf virus (RBSDV) in different host plants and insect vectors: insights from RNA-Seq analysis
10.1186/s12864-024-10649-9 · 2024 · External reference
Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates.
10.1371/journal.ppat.1012163 · 2024 · External reference
Fast and accurate short read alignment with Burrows–Wheeler transform
10.1093/bioinformatics/btp324 · 2009 · External reference
GSAlign: an efficient sequence alignment tool for intra-species genomes
10.1186/s12864-020-6569-1 · 2020 · External reference
Characterisation of putative novel tick viruses and zoonotic risk prediction
10.1002/ece3.10814 · 2024 · External reference
Using strain-resolved analysis to identify contamination in metagenomics data
10.1186/s40168-023-01477-2 · 2023 · External reference
Revisiting a pollen-transmitted ilarvirus previously associated with angular mosaic of grapevine.
10.1016/j.virusres.2024.199362 · 2024 · External reference
Cutadapt removes adapter sequences from high-throughput sequencing reads
10.14806/ej.17.1.200 · 2011 · External reference
MUMmer4: A fast and versatile genome alignment system
10.1371/journal.pcbi.1005944 · 2018 · External reference
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
10.1101/gr.107524.110 · 2010 · External reference
Review on the methodological aspects and potential uses of genomic data mining
10.24072/pci.infections.100248 · 2025 · External reference
IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era
10.1093/molbev/msaa015 · 2020 · External reference
NCBI SRA Toolkit
2024 · External reference
Data mining redefines the timeline and geographic spread of cotton leafroll dwarf virus
10.1094/pdis-06-24-1265-sc · 2024 · External reference
A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand
10.1038/s41467-023-43960-2 · 2024 · External reference
A review of methods for the detection of pathogenic microorganisms
10.1039/c8an01488d · 2019 · External reference
Three-fold expansion of the genetic diversity of blunerviruses through plant (meta)transcriptome data-mining.
10.1016/j.virol.2024.110210 · 2024 · External reference
Diversity and Pathobiology of an Ilarvirus Unexpectedly Detected in Diverse Plants and Global Sequencing Data
10.1094/phyto-12-22-0465-v · 2023 · External reference
Tracing the invertebrate herpesviruses in the global sequence datasets
10.3389/fmars.2023.1159754 · 2023 · External reference
Database resources of the National Center for Biotechnology Information in 2025
10.1093/nar/gkae979 · 2025 · External reference
GenBank 2023 update
10.1093/nar/gkac1012 · 2023 · External reference
Indexing and searching petabase-scale nucleotide resources
10.1038/s41592-024-02280-z · 2024 · External reference
Probing of plant transcriptomes reveals the hidden genetic diversity of the family Secoviridae
10.1007/s00705-024-06076-6 · 2024 · External reference
From the discovery of a novel arepavirus in diseased arecanut palms (Areca catechu L.) in India to the identification of known and novel arepaviruses in bee and plant transcriptomes through data-mining
10.1016/j.virol.2024.110256 · 2024 · External reference
Producing polished prokaryotic pangenomes with the Panaroo pipeline
10.1186/s13059-020-02090-4 · 2020 · External reference
Bioinformatics Goes Viral: I. Databases, Phylogenetics and Phylodynamics Tools for Boosting Virus Research
10.3390/v16091425 · 2024 · External reference
Comparison of Serological and Molecular Methods With High-Throughput Sequencing for the Detection and Quantification of Grapevine Fanleaf Virus in Vineyard Samples
10.3389/fmicb.2018.02726 · 2018 · External reference
Breaking Through Biology’s Data Wall: Expanding the Known Tree of Life by Over 10x using a Global Biodiscovery Pipeline
10.1101/2025.06.11.658620 · 2025 · External reference
Improved metagenomic analysis with Kraken 2
10.1186/s13059-019-1891-0 · 2019 · External reference
Host range and emerging and reemerging pathogens.
10.3201/eid1112.050997 · 2005 · External reference
Virome Characterization of Native Wild-Rice Plants Discovers a Novel Pathogenic Rice Polerovirus With World-Wide Circulation.
10.1111/pce.15204 · 2025 · External reference
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
10.1101/gr.074492.107 · 2008 · External reference
In-depth analysis of 17,115 rice transcriptomes reveals extensive viral diversity in rice plants
10.1038/s41467-025-56769-y · 2025 · External reference