Publication
Real-time monitoring and analysis of SARS-CoV-2 nanopore sequencing with minoTour
Publisher:
Cold Spring Harbor Laboratory
Date:
13-09-2021
DOI:
10.1101/2021.09.13.459777
Abstract: The ongoing SARS-CoV-2 pandemic has demonstrated the utility of real-time analysis of sequencing data, with a wide range of databases and resources for analysis now available. Here we show how the real-time nature of Oxford Nanopore Technologies sequencers can accelerate consensus generation, lineage and variant status assignment. We exploit the fact that multiplexed viral sequencing libraries quickly generate sufficient data for the majority of s les, with diminishing returns on remaining s les as the sequencing run progresses. We demonstrate methods to determine when a sequencing run has passed this point in order to reduce the time required and cost of sequencing. We extended MinoTour, our real-time analysis and monitoring platform for nanopore sequencers, to provide SARS-CoV2 analysis using ARTIC network pipelines. We additionally developed an algorithm to predict which s les will achieve sufficient coverage, automatically running the ARTIC medaka informatics pipeline once specific coverage thresholds have been reached on these s les. After testing on run data, we find significant run time savings are possible, enabling flow cells to be used more efficiently and enabling higher throughput data analysis. The resultant consensus genomes are assigned both PANGO lineage and variant status as defined by Public Health England. S les from within in idual runs are used to generate phylogenetic trees incorporating optional background s les as well as summaries of in idual SNPs. As minoTour uses ARTIC pipelines, new primer schemes and pathogens can be added to allow minoTour to aid in real-time analysis of pathogens in the future. Source code and documentation is available at github.com/LooseLab/minotourapp . Supplementary data are available from github.com/LooseLab/artic_minotour_analyses .