Welcome to INSaFLU’s documentation!


INSaFLU (“INSide the FLU”) is a bioinformatics free web-based suite that deals with primary data (reads) towards the automatic generation of the output data that are actually the core first-line “genetic requests” for effective and timely influenza and SARS-CoV-2 laboratory surveillance. Data integration is continuously scalable, fitting the need for a real-time genomic surveillance during the flu and COVID-19 epidemics.


  • open to all, free of charge, user-restricted accounts
  • applicable to NGS data collected from any amplicon-based schema
  • allows advanced, multi-step software intensive analyses in a user-friendly manner without previous training in bioinformatics
  • automatic identification of influenza type and subtype/lineage, detection of putative mixed infections and intra-host minor variants
  • allows integrating data in a cumulative manner, thus fitting the analytical dynamics underlying the continuous epidemiological surveillance during flu epidemics
  • outputs are provided in nomenclature-stable and standardized formats and can be explored in situ or through multiple compatible downstream applications for fine-tune data analysis and visualization

How to Cite

If you use INSaFLU in your work, please cite this publication:

Borges V, Pinheiro M et al. Genome Medicine (2018) 10:46



If you have any questions, comments or suggestions, please contact us: <vitor.borges@insa.min-saude.pt> or <j.paulo.gomes@insa.min-saude.pt>