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Shotgun Metagenomics with Nephele

Learning Objectives

  • Gain hands-on experience setting up and running a shotgun metagenomics pipeline using Nephele, NIAID’s free application for microbiome analysis.
  • Explore key outputs for downstream analysis.

A Nephele account is required for hands-on participation. Need a Nephele account? See How to register for Nephele for further instructions.

Presentation Slides

Step-by-step instructions to reference during the demo are available in the presentation slides.

Data

Demo Data

Demo data for this workshop are available in CAMI_sub25k_dataset_and_mapping_file.zip. Simply, click the link to download the zipped file. This zip file contains a mapping file and subsampled fastq files from CAMI Toy Human Microbiome Project dataset.

Example Output

Example output files from the demo are available in QC_demo_results.zip and WGSA2_demo_results.zip. These zipped files contain example outputs from QC and WGSA2 pipelines, respectively, using the demo dataset. Simply, click the links to download the zipped files.