ArticleViruses2018
Considerations for Optimization of High-Throughput Sequencing Bioinformatics Pipelines for Virus Detection.
Article in Viruses, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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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.
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Who cites it
16 citing papers in PubMed.
- Validation of an In-House High-Throughput Total RNA Sequencing Test for the Detection of Plant Viruses and Viroids.Viruses · 2026Article
- Viral Clearance: Safety and Efficiency of Biopharmaceuticals.Therapeutic innovation & regulatory science · 2026Review
- Detecting poliovirus sequences in the sequence read archive database using bioinformatics tools.Frontiers in bioinformatics · 2026Article
- Evaluation of high-throughput sequencing for replacing the conventional adventitious virus detection assays used for biologics.NPJ vaccines · 2025Article
- Report of the fourth conference on next-generation sequencing (NGS) for adventitious virus detection in biologics for humans and animals: Validation and implementation of NGS.Biologicals : journal of the International Association of Biological Standardization · 2025Article
- Virus detection by short read high throughput sequencing in a high virus low cellular background.NPJ vaccines · 2025Article
- Report of the third conference on next-generation sequencing for adventitious virus detection in biologics for humans and animals.Biologicals : journal of the International Association of Biological Standardization · 2023Article
- Viruses participate in the organomineralization of travertines.Scientific reports · 2023Article
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- LABRADOR-A Computational Workflow for Virus Detection in High-Throughput Sequencing Data.Viruses · 2021Article
- A potential prognostic model based on miRNA expression profile in The Cancer Genome Atlas for bladder cancer patients.Journal of biological research (Thessalonike, Greece) · 2020Article
- Report of the second international conference on next generation sequencing for adventitious virus detection in biologics for humans and animals.Biologicals : journal of the International Association of Biological Standardization · 2020Article
- Sensitivity and breadth of detection of high-throughput sequencing for adventitious virus detection.NPJ vaccines · 2020Article
- High-Throughput Sequencing for Deciphering the Virome of Alfalfa (Frontiers in microbiology · 2020Review
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Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing (HTS) has demonstrated capabilities for broad virus detection based upon discovery of known and novel viruses in a variety of samples, including clinical, environmental, and biological. An important goal for HTS applications in biologics is to establish parameter settings that can afford adequate sensitivity at an acceptable computational cost (computation time, computer memory, storage, expense or/and efficiency), at critical steps in the bioinformatics pipeline, including initial data quality assessment, trimming/cleaning, and assembly (to reduce data volume and increase likelihood of appropriate sequence identification). Additionally, the quality and reliability of the results depend on the availability of a complete and curated viral database for obtaining accurate results; selection of sequence alignment programs and their configuration, that retains specificity for broad virus detection with reduced false-positive signals; removal of host sequences without loss of endogenous viral sequences of interest; and use of a meaningful reporting format, which can retain critical information of the analysis for presentation of readily interpretable data and actionable results. Furthermore, after alignment, both automated and manual evaluation may be needed to verify the results and help assign a potential risk level to residual, unmapped reads. We hope that the collective considerations discussed in this paper aid toward optimization of data analysis pipelines for virus detection by HTS.
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Registered trials
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