ArticleGigaScience2019
Ultra-deep, long-read nanopore sequencing of mock microbial community standards.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 157 papers.
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Who cites it
157 citing papers in PubMed.
- Review
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- Evolving Approaches to Bacterial Identification: A Review of Classical and Modern Techniques.International journal of molecular sciences · 2026Review
- Integrated approaches for pathogen monitoring and shotgun metagenomic analysis in Atlantic salmon farming.Scientific reports · 2026Article
- Exploring the functional microbiome of pigs within the porcine respiratory disease complex: viral-bacterial co-infections and virulence factor profiling.Microbiology spectrum · 2026Article
- Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.bioRxiv : the preprint server for biology · 2026Article
- Strain-level metagenomic profiling using pangenome graphs with PanTax.Genome research · 2026Article
- Unlocking the full potential of nanopore sequencing: tips, tricks, and advanced data analysis techniques.Nucleic acids research · 2026Review
- Predator avoidance promotes interbacterial symbiosis with myxobacteria in polymicrobial communities.The ISME journal · 2026Article
- EasyAmplicon 2: Expanding PacBio and Nanopore Long Amplicon Sequencing Analysis Pipeline for Microbiome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Sequenoscope: a modular tool for nanopore adaptive sequencing analytics and beyond.Access microbiology · 2026Article
- Bacterial community adaptation after brackish and freshwater coalescence.ISME communications · 2026Article
- Whole genome sequence of Staphylococcus aureus strain 37 M isolated from cows with subclinical mastitis in Uganda.BMC genomic data · 2025Article
- RAmpSim: A Thermodynamic Simulator for Hybridization Capture in Metagenomic Sequencing.bioRxiv : the preprint server for biology · 2025Article
- Benchmarking of human read removal strategies for viral and microbial metagenomics.Cell reports methods · 2025Article
- Real-time analysis and visualization of nanopore metagenomic samples with MARTi.Genome research · 2025Article
- Rapid Nanopore Sequencing of Positive Blood Cultures Using Automated Benzyl-Alcohol Extraction Improves Time-Critical Sepsis Management.Antibiotics (Basel, Switzerland) · 2025Article
- SKiM: accurately classifying metagenomic ONT reads in limited memory.Bioinformatics (Oxford, England) · 2025Article
- The Kocurious case of Noodlococcus: genomic insights intoMicrobial genomics · 2025Article
97 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
backgroundLong sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best approaches for analysis of long-read metagenomic data are unknown. Additionally, rigorous evaluation of bioinformatics tools is hindered by a lack of long-read data from validated samples with known composition.
findingsWe sequenced 2 commercially available mock communities containing 10 microbial species (ZymoBIOMICS Microbial Community Standards) with Oxford Nanopore GridION and PromethION. Both communities and the 10 individual species isolates were also sequenced with Illumina technology. We generated 14 and 16 gigabase pairs from 2 GridION flowcells and 150 and 153 gigabase pairs from 2 PromethION flowcells for the evenly distributed and log-distributed communities, respectively. Read length N50 ranged between 5.3 and 5.4 kilobase pairs over the 4 sequencing runs. Basecalls and corresponding signal data are made available (4.2 TB in total). Alignment to Illumina-sequenced isolates demonstrated the expected microbial species at anticipated abundances, with the limit of detection for the lowest abundance species below 50 cells (GridION). De novo assembly of metagenomes recovered long contiguous sequences without the need for pre-processing techniques such as binning.
conclusionsWe present ultra-deep, long-read nanopore datasets from a well-defined mock community. These datasets will be useful for those developing bioinformatics methods for long-read metagenomics and for the validation and comparison of current laboratory and software pipelines.
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