How do I cite CZ ID (formerly IDseq)?

Use the following references to cite CZ ID:

• mNGS Illumina pipeline:
  • KL Kalantar, et al.: IDseq—an open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. GigaScience 9.10 (2020): giaa111
• mNGS Nanopore pipeline:
  • SE Simmonds, et al.: CZ ID: a cloud-based, no-code platform enabling advanced long read metagenomic analysis. bioRxiv, 2024. doi.org/10.1101/2024.02.29.579666

You can also cite papers that have details about the product and mNGS Illumina pipeline:

• S Saha, et al.: Unbiased metagenomic sequencing for pediatric meningitis in Bangladesh reveals neuroinvasive Chikungunya virus outbreak and other unrealized pathogens. mBio, 2019. 10:10.1128/mbio.02877-19 
• A Ramesh et al.: Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda. PLOS ONE, 2019. doi.org/10.1371/journal.pone.0218318

Our open-source Github repo can be found here.

We love to hear if you’ve used CZ ID in your analysis. Feel free to reach out to us by using the "Contact Us" link in the drop-down menu on your profile if you have questions or feedback.