ArticleJournal of virological methods2020
Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses.
Article in Journal of virological methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed, 35 citations in OpenAlex.
- Advancing the Diagnosis of Non-Hodgkin Lymphoma Through Next-Generation Sequencing in Developing Countries: An Evaluation of Progress-A Narrative Review.Health science reports · 2026Article
- A targeted next-generation sequencing panel for identification of clinically relevant mutation profiles in solid tumours.Scientific reports · 2025Article
- Compatibility of whole-genome sequencing data from Illumina and Ion Torrent technologies in genome comparison analysis ofMicrobial genomics · 2025Article
- Early Detection, Precision Treatment, Recurrence Monitoring: Liquid Biopsy Transforms Colorectal Cancer Therapy.Current cancer drug targets · 2025Review
- Reflective Evaluation of Next-Generation Sequencing Data during Early Phase Detection of the Delta Variant.OBM genetics · 2025Article
- Sequencing and Optical Genome Mapping for the Adventurous Chemist.Chemical & biomedical imaging · 2024Review
- Review
- An Automated Real-Time PCR Assay versus Next-Generation Sequencing in the Detection ofDiagnostics (Basel, Switzerland) · 2024Article
- Benchmarking and improving the performance of variant-calling pipelines with RecallME.Bioinformatics (Oxford, England) · 2023Article
- The Clinical and Genetic Characteristics ofInternational journal of molecular sciences · 2023Article
- Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases.Cells · 2023Review
- Revolutionized virome research using systems microbiology approaches.Experimental biology and medicine (Maywood, N.J.) · 2022Review
- Article
- Method for quick DNA barcode reference library construction.Ecology and evolution · 2021Article
- Article
- High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings.Small methods · 2021Review
- Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function.Frontiers in microbiology · 2021Review
- A theoretical and generalized approach for the assessment of the sample-specific limit of detection for clinical metagenomics.Computational and structural biotechnology journal · 2021Article
- Identification of Recurrent Mutations in the microRNA-Binding Sites of B-Cell Lymphoma-Associated Genes in Follicular Lymphoma.International journal of molecular sciences · 2020Article
- Microbiome Composition andTropical medicine and infectious disease · 2020Article
Corrections and comments
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Authors and funding
13 authors at 3 institutions in 1 country.
Funding
Abstract
Next-generation sequencing is a powerful tool for virological surveillance. While Illumina® and Ion Torrent® sequencing platforms are used extensively for generating viral RNA genome sequences, there is limited data comparing different platforms. The Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5 platforms were evaluated using a panel of sixteen specimens containing picornaviruses and human caliciviruses (noroviruses and sapoviruses). The specimens were processed, using combinations of three library preparation and five sequencing kits, to assess the quality and completeness of assembled viral genomes, and an estimation of cost per sample to generate the data was calculated. The choice of library preparation kit and sequencing platform was found to impact the breadth of genome coverage and accuracy of consensus viral genomes. The Ion Torrent S5 510 chip runs produced more reads at a lower cost per sample than the highest output Ion Torrent PGM 318 chip run, and generated the highest proportion of reads for enterovirus D68 samples. However, indels at homopolymer regions impacted the accuracy of consensus genome sequences. For lower throughput sequencing runs (i.e., Ion Torrent 510 and Illumina MiSeq Nano V2), the cost per sample was lower on the MiSeq platform, whereas with higher throughput runs (Ion Torrent 530 and Illumina MiSeq V2) there is less of a difference in the cost per sample between the two sequencing platforms ($5.47-$10.25 more per sample for an Ion Torrent 530 chip run when multiplexing 24 samples). These findings suggest that the Ion Torrent S5 and Illumina MiSeq platforms are both viable options for genomic sequencing of RNA viruses, each with specific advantages and tradeoffs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.