Abstract
Metagenomic sequencing combined with Oxford Nanopore Technology has the potential to become a point-of-care test for infectious disease in public health and clinical settings, providing rapid diagnosis of infection, guiding individual patient management and treatment strategies, and informing infection prevention and control practices. However, publicly available, streamlined, and reproducible pipelines for analyzing Nanopore metagenomic sequencing data are still lacking. Here we introduce NanoSPC, a scalable, portable and cloud compatible pipeline for analyzing Nanopore sequencing data. NanoSPC can identify potentially pathogenic viruses and bacteria simultaneously to provide comprehensive characterization of individual samples. The pipeline can also detect single nucleotide variants and assemble high quality complete consensus genome sequences, permitting high-resolution inference of transmission. We implement NanoSPC using Nextflow manager within Docker images to allow reproducibility and portability of the analysis. Moreover, we deploy NanoSPC to our scalable pathogen pipeline platform, enabling elastic computing for high throughput Nanopore data on HPC cluster as well as multiple cloud platforms, such as Google Cloud, Amazon Elastic Computing Cloud, Microsoft Azure and OpenStack. Users could either access our web interface (https://nanospc.mmmoxford.uk) to run cloud-based analysis, monitor process, and visualize results, as well as download Docker images and run command line to analyse data locally.
Highlights
Oxford Nanopore Technology (ONT) is a third generation sequencing technology with the advantage of generating real-time, long read data with highly portable devices.Nanopore sequencing has been successfully applied in a broad range of research areas, including human genetics, cancer, microbiology, plant, and infectious diseases [1,2,3,4,5]
Metagenomic sequencing with ONT has the potential to become a point-of-care test for infectious diseases in clinical and public health settings, providing rapid diagnosis of infection, guide individual patient management and treatment strategies, and informing infection prevention and control practices [12,13,14]
Nanopore metagenomic sequencing of the novel coronavirus disease 2019 (COVID-19) that causes the ongoing pandemic in the world has provided critical and timely evidence for human-to-human transmission of this virus [15]
Summary
Oxford Nanopore Technology (ONT) is a third generation sequencing technology with the advantage of generating real-time, long read data with highly portable devices.Nanopore sequencing has been successfully applied in a broad range of research areas, including human genetics, cancer, microbiology, plant, and infectious diseases [1,2,3,4,5]. Oxford Nanopore Technology (ONT) is a third generation sequencing technology with the advantage of generating real-time, long read data with highly portable devices. On-site sequencing with ONT has enabled real-time surveillance and tracking of Ebola, Zika and Lassa epidemics [6,7,8]. Metagenomic sequencing has the capacity to detect all potential pathogens from individual clinical samples, and provide genomic information for comprehensive characterization of the pathogens, microbiome analyses, and investigation of epidemiology and transmission [9,10,11]. Metagenomic sequencing with ONT has the potential to become a point-of-care test for infectious diseases in clinical and public health settings, providing rapid diagnosis of infection, guide individual patient management and treatment strategies, and informing infection prevention and control practices [12,13,14]. Nanopore metagenomic sequencing of the novel coronavirus disease 2019 (COVID-19) that causes the ongoing pandemic in the world has provided critical and timely evidence for human-to-human transmission of this virus [15]
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