Abstract Background As the use of nanopore sequencing for metagenomic analysis increases, tools capable of performing long-read taxonomic classification in a fast and accurate manner are needed. Existing tools were either designed for short-read data (eg. Centrifuge) or take days to analyse modern sequencer outputs (eg. MetaMaps). Results We present BugSeq, a novel, highly accurate metagenomic classifier for nanopore reads. BugSeq (F1=0.91-0.95) offers better read classification than MetaMaps (F1=0.89-0.94) in a fraction of the time. BugSeq significantly improves on the accuracy of Centrifuge (F1=0.79-0.93) while offering competitive run times. We apply BugSeq to metagenomic sequencing of 41 samples from patients with lower respiratory tract infections and show that it produces greater concordance with microbiological culture and qPCR compared with “What’s In My Pot” analysis. Conclusion BugSeq is deployed to the cloud for easy and scalable long-read metagenomic analyses. BugSeq is freely available for non-commercial use at https://bugseq.com/free . Contact sam@bugseq.com

BugSeq: a highly accurate cloud platform for long-read metagenomic analyses