From “reads” to viral metagenomics detection and routine genomic surveillance

INSaFLU (“INSide the FLU”) is a free bioinformatics web-based (also locally installable) suite that deals with primary sequencing data (Illumina, Ion Torrent and Oxford Nanopore Technologies reads) towards:
  • metagenomics virus detection (from reads to virus detection).
  • routine genomic surveillance (from reads to mutation detection, consensus generation, virus classification, alignments, “genotype-phenotype”, screening, phylogenetics, integrative Nextstrain phylogeographical and temporal analysis etc).
INSaFLU-TELEVIR versatility and functionality is expected to supply public health laboratories and researchers with a user-oriented “start-to-end” bioinformatics framework that can potentiate a strengthened and timely detection and monitoring of viral (emerging) threats.
Virus Detection

From Reads to viral detection

Reference-based genome assembly

From reads to consensus sequence, mutations list, alignments, Pango lineage classification, etc.


From consensus sequences to phylogeographic and temporal analysis and metadatada navigation

Future Directions

INSaFLU is under active development in order to have additional features, such as modules to automatically detect virus reassortment and to perform temporal and geographical data integration 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


INSaFLU development is being co-funded by the European Commission on behalf of OneHealth EJP TELE-Vir project.


We thank the Infraestrutura Nacional de Computação Distribuída (INCD) for providing computational resources for testing the INSaFLU platform. INCD was funded by FCT and FEDER under the project 22153-01/SAICT/2016


If you have any questions, comments or suggestions, please contact us:

vitor.borges at j.paulo.gomes at