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Andrey Kislyuk edited this page Feb 25, 2021
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IDseq 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. Check out our repositories:
- idseq-web - Frontend portal
- idseq-dag - Bioinformatics pipeline and workflow engine (here)
- idseq-cli - Command line upload interface
- idseq-bench - Pipeline benchmarking tools
The documentation presented here reflects the current IDseq pipeline status and processes, with descriptions of the parameters used. It is divided into three main analysis sections.
- Host Filtering and QC
- Alignment and Taxonomic Aggregation
- 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.