Rampart for DENV sequencing

Rampart is a browser-based dashboard for live analysis of nanopore (MinION) sequencing runs. As basecalled reads stream off the sequencer, Rampart assigns them to reference genomes in real time, visualises per-sample coverage, and shows which barcoded sample is producing data – letting field labs decide on the fly whether a run is working, whether sufficient coverage has been achieved, which samples need more time, and which serotype they're looking at.

The DeZi adaptation extends the standard Rampart template with reference genomes for DENV-1, DENV-2, DENV-3 and DENV-4, paired with the ARTIC2/DeZi pan-dengue primer scheme. Operators see, within minutes of a run starting, which serotype is being sequenced — useful in clinical or outbreak contexts where the serotype is initially unknown. Rampart was first deployed during the Ebola response in DRC and the yellow fever outbreak in Brazil, and was widely adopted during the SARS-CoV-2 pandemic. This dengue template offers the same real-time advantage to laboratories sequencing DENV directly from clinical samples.