Nephele DADA2 Workflow

To download the practice dataset provided by Nephele, visit: https://nephele.niaid.nih.gov/user_guide_data/

Download the first set of sequences listed as well as the mapping file.

The reference provided for this set of sequences is listed as: Experimental Microbial Dysbiosis Does Not Promote Disease Progression in SIV-Infected Macaques. NCBI BioProject: PRJNA417022

Once downloaded, unzip the downloaded file and ensure all .fastq.gz files are present.

Click the Home tab.

Choose the Analyze option.

Under Amplicon Metagenomics , select "Start job" option under DADA2 .

Select Paired End FASTQ , as this is a paired-end dataset.

Click "Upload from my computer" and add all .fastq.gz files from the downloaded dataset. Start upload

Select "Next" and upload the corresponding Mapping File.

After reaching the Pipeline Selection page, click Select and enter a description of the job.

Keep Filter and Trim, Merge Pairs, and Analysis settings defaulted. Do not check Ion Torrent Data. Click Validate and Submit *Note: This is for following the exact tutorial instructions. If you would like to make changes to these pre-sets, proceed with these changes.

Nephele will send an email upon job completion.

From the My Workspace tab, hover to the view results icon under Actions for the completed DADA2 job.

Under Reported Statistics, Reported Files, Reported Images, Reported Tables, and Reported Charts and explore outputs.

Reported files of note include: Rooted tree, Rarefaction curve, Alpha diversity, PCoA binomial, BCoA Bray-Curtis, and ASV heatmap.

Reported images of note include: Quality profiles of forward and reverse reads

Reported tables of note include: Read counts by sample and Top species table

Reported charts of note include: Reads in vs. reads out and Track reads