NCM 2022: CZ ID: an open-source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring

Metagenomic next-generation sequencing (mNGS) has transformed disease surveillance by enabling the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. While Oxford Nanopore sequencers have transformed the ability to track diseases during outbreaks by providing compact and portable sequencing technology, long-read methods offer specific challenges for successful implementation of metagenomics within the context of disease surveillance. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Most mNGS data analysis tools require bioinformatics expertise and access to local server-class hardware resources which presents an obstacle for many research laboratories, especially in resource-limited environments. Here, we describe the CZ ID portal, which is an open-source cloud-based metagenomics pipeline and web application that overcomes these barriers and provides a service for global pathogen detection and monitoring.