microbiome

Microbiome Data Analysis and Nephele Demo

Nephele Web Server

https://nephele.niaid.nih.gov

Resources for RML session on Microbiome Data Analysis

1. Slides - download pdf of slides here

2. Test input files: for 16S pipelines Download sequences and mapping files from "How to submit a job" - https://nephele.niaid.nih.gov/user_guide/

Steps to run Demo. For more details see: https://nephele.niaid.nih.gov/user_guide/

1. Request account in nephele server
2. Select Amplicon Data, 16S
3. Sign into Nephele with the email you registered with, then select Paired End Fastq
4. Select "Upload files from publicly accessible URL(s)", Upload via FTP . Provide the following path ftp://helix.nih.gov/pub/mqbcbb/nepheleFQ/ Please know that this folder will be available only temporarily from this FTP location.
5. Download file from ftp://helix.nih.gov/pub/mqbcbb/N2_16S_mapping.xlsx then upload to Nephele as the mapping file.
6. Follow along to submit a job. THere is no need to change default parameters for this dataset.
7. Expect an email with words "nephele pipeline success"

View results

1. Download DADA2 example output here

2. Alternatively, if you run the job, expect an email with note that job has completed https://nephele.niaid.nih.gov/results/f04730b61840