EMtrace: offline nanopore metagenomics on a laptop for rapid viral diagnostics, genome recovery and 16S profiling

Nanopore sequencers produce reads within minutes, but metagenomic analysis remains challenging where internet access is limited, data are sensitive or computing resources are modest. EMtrace is an offline pipeline that runs on a laptop during sequencing: it classifies MinKNOW reads, estimates taxon abundance by expectation-maximization (EM) and assembles reference-based consensus genomes. We benchmarked it against five virome and four 16S rRNA tools on simulated, mock-community and clinical data. On field isolates and 16 SARS-CoV-2 clinical samples, EMtrace had the highest species-level F1 score (1.00 and 0.97) and one false-positive species, against 3-7 for the comparators. It recovered divergent viruses as completely as ViMOP, and low-titre field libraries more completely, at [≥]99.7% identity. In replayed runs, it identified the target virus in the first 4,000-read batch (5-13 min). With a shared 16S reference, EMtrace reported two to three times fewer false-positive species than Emu.