Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses

Marta Ibañez-Lligoña, Sergi Colomer-Castell, Alejandra González-Sánchez, Josep Gregori, Carolina Campos, Damir Garcia-Cehic, Cristina Andrés, Maria Piñana, Tomàs Pumarola, Francisco Rodríguez-Frias, Andrés Antón, Josep Quer*

*Corresponding author for this work

Research output: Contribution to journalReview articleResearchpeer-review

5 Citations (Scopus)


Epidemics and pandemics have occurred since the beginning of time, resulting in millions of deaths. Many such disease outbreaks are caused by viruses. Some viruses, particularly RNA viruses, are characterized by their high genetic variability, and this can affect certain phenotypic features: tropism, antigenicity, and susceptibility to antiviral drugs, vaccines, and the host immune response. The best strategy to face the emergence of new infectious genomes is prompt identification. However, currently available diagnostic tests are often limited for detecting new agents. High-throughput next-generation sequencing technologies based on metagenomics may be the solution to detect new infectious genomes and properly diagnose certain diseases. Metagenomic techniques enable the identification and characterization of disease-causing agents, but they require a large amount of genetic material and involve complex bioinformatic analyses. A wide variety of analytical tools can be used in the quality control and pre-processing of metagenomic data, filtering of untargeted sequences, assembly and quality control of reads, and taxonomic profiling of sequences to identify new viruses and ones that have been sequenced and uploaded to dedicated databases. Although there have been huge advances in the field of metagenomics, there is still a lack of consensus about which of the various approaches should be used for specific data analysis tasks. In this review, we provide some background on the study of viral infections, describe the contribution of metagenomics to this field, and place special emphasis on the bioinformatic tools (with their capabilities and limitations) available for use in metagenomic analyses of viral pathogens.

Original languageEnglish
Article number587
Number of pages15
Issue number2
Publication statusPublished - 20 Feb 2023


  • deep-sequencing
  • diagnostic tools
  • metagenomics
  • NGS
  • viruses
  • zoonosis
  • Metagenomics
  • Pandemics
  • Computational Biology
  • Antiviral Agents
  • Viruses/genetics


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