Viroscope: plant viral diagnosis from NGS data using biologically-informed genome assembly coverage
Valenzuela, S. L.; Norambuena, T.; Morgante, V.; Garcia, F.; Jimenez, J. C.; Nunez, C.; Fuentes, I.; Pollak, B.
Show abstract
Next-generation sequencing (NGS) methods are transforming our capacity to detect pathogens and perform disease diagnosis. Although sequencing advances have enabled accessible and point-of-care NGS, data analysis pipelines have yet to provide robust tools for precise and certain diagnosis, particularly in cases of low sequencing coverage. Lack of standardized metrics and harmonized detection thresholds confound the problem further, impeding the adoption and implementation of these solutions in real-world applications. In this work, we tackle these issues and propose biologically-informed viral genome assembly coverage as a method to improve diagnostic certainty. We use the identification of viral replicases, an essential function of viral life cycles, to define genome coverage thresholds in which biological functions can be described. We validate the analysis pipeline, Viroscope, using field samples, synthetic and published datasets and demonstrate that it provides sensitive and specific viral detection. Furthermore, we developed Viroscope.io a web-service to provide on-demand NGS data viral diagnosis to facilitate adoption and implementation by phytosanitary agencies to enable precise viral diagnosis.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Novel NGS Pipeline for Virus Discovery from a Wide Spectrum of Hosts and Sample Types 96%
- Latest RNA and DNA nanopore sequencing allows for rapid avian influenza profiling 95%
- An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany 95%
Similar papers in this journal
- Structural variation turnovers and defective genomes: key drivers for the in vitro evolution of the large double-stranded DNA koi herpesvirus (KHV) 95%
- EnVhogDB: an extended view of the viral protein families on Earth through a vast collection of HMM profiles 93%
- COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences 92%
Similar papers in this journal
- Interplay between a polerovirus and a closterovirus decreases aphid transmission of the polerovirus 93%
- Revisiting rustrela virus - new cases of encephalitis and a solution to the capsid enigma 92%
- Genetic diversity and characterization of circular replication(Rep)-encoding single-stranded (CRESS) DNA viruses 91%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.