Phase II - ​Expanding with sentinel surveillance sites

SeqAfrica began its second phase in October 2023. A focus of SeqAfrica Phase II will be to democratize sequencing, which will be achieved by expanding our network. We pilot 6 sentinel sites focusing on ONT long-read sequencing, while still maintaining our network of regional sequencing centers. SeqAfrica will employ a solution tailored to meet the African challenges of unreliable internet and limited number of trained bioinformatitians by pairing  a minION device with a laptop with the MinKNOW software and an approach to data analysis fit for non or novel-users. Experiences gathered during a scoping period and initial pilot phase will determine the standard operating procedures for data analysis at sentinel surveillance sites.

Available analysis solutions

An offline solution

​The Microbial Outbreak Surveillance System (MOSS) is an offline desktop-based system providing automated analyses of ONT long-read data. MOSS is an easy-to-use system made for non-technical users running localized on a laptop.  The MOSS program employs CGE tools to type AMR genes. virulence factors, plasmids, and MLST of genomic data from clinical bacterial isolates and outputs a PDF report of the results. The result report is designed for easy to read for individuals with no or limited bioinformatic and genomic training like e.g., microbiologist and physicians. Read more about the MOSS system here.

Cloud based solution

The Terra lorem ipsum. 


​Information presented on this website is considered public information (unless otherwise noted) and may be distributed or copied. Use of appropriate byline/photo/image credit is requested. While The National Food Institute makes every effort to provide accurate and complete information, various data such as names, telephone numbers, etc. may change prior to updating. The National Food Institute welcomes suggestions on how to improve our home page and correct errors. The National Food Institute provides no warranty, expressed or implied, as to the accuracy, reliability or completeness of furnished data.

Some of the documents on this server may contain live references (or pointers) to information created and maintained by other organizations. Please note that The National Food Institute does not control and cannot guarantee the relevance, timeliness, or accuracy of these outside materials.


Technical University of Denmark, National Food Institute

CVR: 30060946



DK-2800 Lyngby

Kemitorvet Building 204​

Contact us

Tlf.: +45 3588 6601