https://github.com/niaid/microbiome
Microbiome Data Analysis and Nephele Demo
https://github.com/niaid/microbiome
bcbb-training microbiome microbiome-analysis
Last synced: 4 months ago
JSON representation
Microbiome Data Analysis and Nephele Demo
- Host: GitHub
- URL: https://github.com/niaid/microbiome
- Owner: niaid
- Created: 2019-09-05T16:10:17.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2019-09-12T05:36:52.000Z (over 6 years ago)
- Last Synced: 2025-08-12T00:47:28.024Z (10 months ago)
- Topics: bcbb-training, microbiome, microbiome-analysis
- Homepage:
- Size: 14.6 KB
- Stars: 1
- Watchers: 5
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# microbiome
Microbiome Data Analysis and Nephele Demo
### Nephele Web Server
### Resources for RML session on Microbiome Data Analysis ###
1. Slides - [download pdf of slides here](https://proj-bip-prod-publicread.s3.amazonaws.com/training/Microbiome+and+Nephele/Microbiome_RML.pdf)
2. Test input files: for 16S pipelines
Download sequences and mapping files from "How to submit a job" -
#### 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 **** 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](https://nephele-prod-testdata.s3.amazonaws.com/dada_example_output.zip)
2. Alternatively, if you run the job, expect an email with note that job has completed