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Metagenomic Analysis

Metagenomic Analysis

Access step-by-step guides to perform mNGS analysis.

Upload Data

Data File Requirements
Upload Data through the Web App
Upload Data Using Command Line
Upload Data to Generate Viral Consensus Genomes via Command Line

Quality Control

Sample QC
Background Models

Sample Report

Sample Report Table
Taxonomic Tree View
Filter Sample Report Table
Coverage Visualization
BLAST Taxa
Add Notes (Annotate Hits)

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Consensus Genome

Assemble Viral Consensus Genomes from Sample Report
Consensus Genome Quality Checks
Download Consensus Genome Data
Viral Consensus Genome Pipeline
Generating a viral consensus genome

Heatmap

Creating a Heatmap
Viewing Sample and Taxon Details in the Heatmap
Metadata in the Heatmap
Heatmap Analysis
Heatmap clustering
Saving and Downloading a Heatmap

Phylogenetic Tree

Building a Phylogenetic Tree
Interpreting a Phylogenetic Tree
Why a Pairwise Distance Matrix Instead of a Tree?
Phylogenetic Tree Pipeline for mNGS Samples
Creating a Phylogenetic Tree

Bulk Download

Initiate a Bulk Download
Keep Track of Downloads
Download Via the Command Line

mNGS Pipeline

Pipeline Details
Illumina Pipeline Update: Scaling Up
Illumina Pipeline Update: Relative Abundance Calculation

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