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NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline
Yifei Xu1,2, Fan Yang-Turner1,2, Denis Volk1,2
1Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Nucleic Acids Research
|May 23, 2020
Summary
NanoSPC is a new pipeline for analyzing Nanopore sequencing data, enabling rapid infectious disease diagnosis. This tool aids in identifying pathogens, guiding treatment, and improving infection control in public health.
Area of Science:
- Genomics
- Bioinformatics
- Infectious Disease Surveillance
Background:
- Metagenomic sequencing with Oxford Nanopore Technology offers potential for point-of-care infectious disease diagnostics.
- Existing pipelines for Nanopore metagenomic data analysis lack standardization, reproducibility, and accessibility.
- Rapid and comprehensive pathogen identification is crucial for public health and clinical decision-making.
Purpose of the Study:
- To introduce NanoSPC, a scalable, portable, and cloud-compatible pipeline for Nanopore metagenomic sequencing data analysis.
- To enable simultaneous identification of pathogenic viruses and bacteria for comprehensive sample characterization.
- To facilitate high-resolution inference of transmission through single nucleotide variant detection and genome assembly.
Main Methods:
- Development of NanoSPC using Nextflow and Docker for enhanced reproducibility and portability.
- Deployment of NanoSPC on a scalable platform supporting High-Performance Computing (HPC) clusters and multiple cloud environments (Google Cloud, AWS, Azure, OpenStack).
- Provision of a web interface for cloud-based analysis and command-line options for local data analysis.
Main Results:
- NanoSPC successfully identifies pathogenic viruses and bacteria.
- The pipeline enables detection of single nucleotide variants and assembly of complete consensus genome sequences.
- NanoSPC supports high-throughput Nanopore data analysis across diverse computing infrastructures.
Conclusions:
- NanoSPC addresses the need for streamlined and reproducible analysis of Nanopore metagenomic data.
- The pipeline enhances capabilities for infectious disease diagnosis, patient management, and infection control.
- NanoSPC provides a flexible and accessible solution for pathogen characterization from metagenomic sequencing data.
