Generating microbial insights from nanopore metagenomic data using an open-source, cloud-based metagenomics tool for researchers

CZ ID is a free cloud-based metagenomics analysis platform for researchers. Metagenomics has enabled the rapid, unbiased detection of microbes in various sample types, leading to exciting discoveries in infectious disease, microbiome, and novel virus research. However, the analysis of mNGS data is complex and resource-intensive. With CZ ID, users can upload their raw sequencing data, find matches in the NCBI database, get per-sample taxon counts and perform a variety of analyses and data visualizations. The intuitive interface and interactive visualizations make exploring and interpreting results simple. Initially, CZ ID supported short-read data only, but we saw a rise in demand for a long-read pipeline from researchers, especially in low and middle-income countries. Here we describe our new long-read pipeline that accepts Oxford Nanopore reads and highlight some compelling use cases, including emerging biological threats and characterizing the microbial landscape.

What does the webinar include?

• The Chan Zuckerberg Initiative’s infectious disease program
• Nanopore metagenomics data in an infectious disease setting
• The CZ ID nanopore pipeline
• The advantages of nanopore sequencing for metagenomics
• Previous uses of nanopore sequencing in pathogen surveillance

Meet the speaker

Dr. Sara Simmonds is a Computational Biologist at the Chan Zuckerberg Initiative (CZI), where she works closely with scientists, engineers and the product team to develop open source software for metagenomic (CZ ID) and single-cell (CZ CELLxGENE) applications. Sara is passionate about building computational tools that enable researchers and clinicians to make breakthrough discoveries in their fields, accelerating the pace of science. She strives to incorporate learnings from collaborations with grantees and external scientists into product development. Before joining CZI, Sara held a variety of roles where she honed her skills in bioinformatics. She was a research professor in evolutionary biology and a lead geneticist for endangered salmon species. Her experience in these areas has given her a unique perspective on how computational tools can be used to solve complex biological problems. Sara holds a PhD in Biological Sciences from UCLA, specializing in evolutionary biology and genomics.