NanoSPC

NanoSPC performs integrated analysis of Nanopore sequencing data to detect viral and bacterial pathogens, call single nucleotide variants (SNVs), and assemble consensus genomes for epidemiological and clinical investigations.

Key Features:

• Scalable and Portable Analysis: Implemented in Nextflow and packaged in Docker images to enable reproducible, portable execution across computational platforms.
• Cloud Compatibility: Supports deployment on Google Cloud, Amazon Elastic Compute Cloud (EC2), Microsoft Azure, OpenStack, and HPC clusters to enable elastic computing for high-throughput Nanopore data.
• Comprehensive Pathogen Characterization: Simultaneously identifies potentially pathogenic viruses and bacteria within individual samples for detailed microbial characterization.
• Single Nucleotide Variant Detection and Genome Assembly: Detects single nucleotide variants (SNVs) and assembles high-quality complete consensus genome sequences to support high-resolution inference of transmission pathways.

Scientific Applications:

• Public Health Surveillance: Enables genomic surveillance and outbreak detection through identification and characterization of pathogens from sequencing data.
• Clinical Diagnostics: Provides pathogen identification and genetic variant information to inform rapid diagnosis, patient treatment decisions, and infection control practices.
• Epidemiological Investigations: Facilitates large-scale genomic epidemiology by processing high-throughput Nanopore data for transmission inference and population-level analyses.

Methodology:

Implemented as a Nextflow pipeline executed within Docker images, with support for execution on Google Cloud, Amazon EC2, Microsoft Azure, OpenStack, and HPC clusters, processing Nanopore sequencing data to identify viruses and bacteria, call SNVs, and assemble consensus genomes.