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.

Nextstrain

From consensus sequences to phylogeographic and temporal analysis and metadatada navigation

How to cite

If you use INSaFLU in your work, please cite:

Santos JD, et al. Genome Medicine (2024) 16:61

https://doi.org/10.1186/s13073-024-01334-3

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

https://doi.org/10.1186/s13073-018-0555-0

Funding

The development of INSaFLU-TELEVIR and the expansion of its computational capacity have been co-funded by INSA and various projects promoted by the European Union, namely TELEVIR, GENEO and DURABLE.

Acknowledgments

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

Contacts

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

vitor.borges at insa.min-saude.pt insaflu at insa.min-saude.pt