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CZ ID Workflows

Overview

Infectious Disease Sequencing Platform

CZ ID is a hypothesis-free global software platform that helps scientists identify pathogens in metagenomic sequencing data.

• Discover - Identify the pathogen landscape
• Detect - Monitor and review potential outbreaks
• Decipher - Find potential infecting organisms in large datasets

A collaborative open project of Chan Zuckerberg Initiative and Chan Zuckerberg Biohub.

The documentation presented here reflects the current CZ ID pipeline status and processes, with descriptions of the parameters used. It is divided into three main analysis sections.

1. Host Filtering and QC
2. Alignment and Taxonomic Aggregation
3. Reporting and Visualization

The pipeline relies on a variety of different software, whose versions are listed below. The most up-to-date version information can be found in the Dockerfile.