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Getting Started

• Guide: Data Analysis
• A guide to BLAST

Upload Your Data

• Upload requirements
• Upload on the Web
• Upload with Command Line

Quality Control

• Overview
• Project Page
• Sample QC
• Background Models

Analyze Your Sample

• ★ Generating a viral consensus genome
• Overview
• Pipeline Details
• Single Sample Report Table
• Taxonomic Tree View
• Filtering

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Analyze Multiple Samples

• ★ Creating a Phylogenetic Tree
• Overview
• Creating a Heatmap
• Metadata in the Heatmap
• Viewing Sample and Taxon Details in the Heatmap
• Heatmap Analysis

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Bulk Downloads

• Overview
• Initiate a Bulk Download
• View your Previous & Current Downloads
• Download Via the Command Line
• How to open a tar.gz file

SARS-CoV-2 Consensus genome

• ★ Troubleshooting QC issues
• Video tutorial: How to upload and analyze SARS-CoV-2 consensus genome
• Uploading samples and pipeline overviews
• Building and analyzing a SARS-CoV-2 consensus genome
• Viewing samples in Nextclade
• Initiate a bulk download

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FAQ

• ★ Where can I find more information about the "Known Pathogen" tags?
• How do I cite CZ ID (formerly IDseq)?
• Does CZ ID work with Nanopore reads?
• How do I submit a feature request?
• How do I request a new host genome be added to CZ ID?
• How do I interpret the quality of my ERCC results?

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Pipeline Releases

• Current: Version 4.0