Generating microbial insights from nanopore metagenomic data using CZ ID: a free, open source, cloud-based metagenomics tool for researchers
CZ ID is a free cloud-based platform for metagenomics analysis. It enables researchers to upload sequencing data, find matches in the NCBI database, perform analyses, and visualize results. A new long-read pipeline has been added to support Oxford Nanopore reads, with applications in studying biological threats and microbial landscapes.
Metagenomics have 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.
- The focus of the Chan Zuckerberg Initiative’s Infectious Disease Program
- How to utilize nanopore metagenomics data in an infectious disease setting
- The CZ ID nanopore pipeline through a demo of the platform
- The advantages of nanopore sequencing for metagenomics
- Previous uses of nanopore sequencing in pathogen surveillance
Who may this interest?
- Principal Investigators,
- Researchers
- Postdoctoral fellows
- Application specialists
- Lab supervisors/managers/directors
- Staff scientists
- Bioinformaticians
Speakers
Sara Simmonds
Computational Biologist
Chan Zuckerberg Initiative
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.
Lynn Ly
Bioinformatician
Chan Zuckerberg Initiative
Lynn is a bioinformatician at Oxford Nanopore Techologies in San Francisco. She works in the Emerging Applications group, which is focused on highlighting new biological use cases for nanopore sequencing. Lynn holds a Master’s degree in Integrative Genetics and Genomics from the University of California, Davis.
In association with
This webinar was recorded on Thursday 16 November 2023