From “reads” to viral metagenomics detection and routine genomic surveillance
- 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).
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
Walkthrough INSaFLU by logging into the "demo" account
More information
Documentation: https://insaflu.readthedocs.io/en/latest
Local installation: https://github.com/INSaFLU/docker
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:
Santos JD, et al. Genome Medicine (2024) 16:61
https://doi.org/10.1186/s13073-024-01334-3Borges V, Pinheiro M et al. Genome Medicine (2018) 10:46
https://doi.org/10.1186/s13073-018-0555-0
Funding
INSaFLU development is being co-funded by the European Commission on behalf of OneHealth EJP TELE-Vir project.
https://onehealthejp.eu/jrp-tele-vir/
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
Disclaimer and Privacy Policy
General statement
The INSaFLU portal and its associated resources and outputs are for research, educational and informational purposes only, not for commercial use. It is a non-profit service to the scientific community.
In any case, the name of INSaFLU and its logo shall not be associated with business promotion without prior written approval.
Warranties
In no event is the access to this portal guaranteed.
This portal contains links to external third-party websites. INSaFLU team has not reviewed the contents of these third-party websites and makes no warranty of any kind, expressed or implied, regarding these websites. INSaFLU does not own, monitor, operate or moderate these third-party websites.
The User represents and warrants that he/she/it shall not violate or circumvent any safety program or introduce advertisements containing codes or malware, spyware, data corruption, viruses, data infections or other harmful codes, hacking mechanisms, data crash codes and the like.
INSaFLU team will not use any data submitted to INSaFLU for research, educational, informational, clinical, commercial or any other purpose.
INSaFLU makes no warranties of any kind regarding the accuracy of any data, software and/or database.
Liability
The INSaFLU team is responsible for maintaining and updating the content of INSaFLU. However, INSaFLU team makes no representation or warranty regarding results obtained from using any information, tools or services offered by INSaFLU.
In case of unexpected issues, unexpected disruption, force majeure and similar events, such as: unauthorized or accidental destruction of data; accidental loss; technical faults; forgery, theft or unlawful use; unauthorized alteration, copying, access or other unauthorized processing and the like; violation or circumvention of any safety program or the introduction of advertisements containing codes or malware, spyware, data corruption, viruses, data infections or other harmful codes, hacking mechanisms, data crash codes and the like, by any third party or by any user, the INSaFLU team shall not be held liable for, including but not limited to, any liabilities, losses, loss of profits, data loss, damages, claims, costs and expenses (including legal fees) resulting from such circumstances.
Personal data
While providing us your e-mail upon log into INSaFLU, the INSaFLU team can contact you if you are experiencing any problems with your INSaFLU runs and inform you about INSaFLU updates.
The user is entirely responsible for maintaining the confidentiality of his/her password and account and for all activities that occur under your account. The user agrees to notify the INSaFLU team immediately of any unauthorized use of his/her personal data or of any other breach of security that she/he becomes aware of. The INSaFLU team is not be liable for any loss that you may incur as a result of someone else using your personal account, either with or without your knowledge. The INSaFLU team reserves the right, solely for security reasons to suspend or delete a user account.
The INSaFLU team will neither use any data submitted to INSaFLU for any purpose, nor claim ownership of any data stored by users in their personal space. The INSaFLU team will respect the privacy of the information stored in the private space of the users.
The INSaFLU reserves the right to disable a query if it causing technical problems to its computational infrastructure. Such disabled queries will be reported to the users.
If you would like to delete your account, including any associated data, then contact us via insaflu@insa.min-saude.pt