Call for applications - Microbiome/Metagenome data analysis workshop on May 11

Thursday, April 28, 2022

The Duke Microbiome Center will host a hands-on bioinformatics data analysis workshop focused on learning how to process and analyze 16S rRNA sequencing data. This workshop will also introduce a new computational pipeline developed by DMC members for processing 16S rRNA data that is available to the Duke community via the Duke Compute Cluster. 

Please see the announcement below for information regarding how to apply. An application is required and we will be doing a selection of candidates. We generally are able to select one person per investigator group. If more than one person applies from a lab we may ask the PI to choose one person to attend.

Workshop Description:

16S_pipeline is a bioinformatics best-practice analysis pipeline for 16S rRNA gene sequencing. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

When: Wednesday, May 11th 2022 (9 am – 11 am).

Where: LSRC A155

Instructor:

Jianhong Ou: Jianhong.ou@duke.edu

Learning Goals:

  1. Gain the knowledge of typical workflows for the 16S rRNA gene sequencing analysis.
  2. Learn how to test run 16S_pipeline.
  3. Learn how to run 16S_pipeline for real data.
  4. Learn how to adjust the parameters to fit your experiment design.

Learning Objectives: 

  1. Learn how to set up the conda environment on cluster.
  2. Learn how to set up the test run.
  3. Learn how to set up the run for real size data.
  4. Understand how to adjust the parameters.
  5. Understand how to get help.

Time Outline: 

  • Activity
  • Time
  • Introduction of 16S_pipeline
  • 30min
  • Sample code explanation
  • 10min
  • Hands-on workshop
  • 90min
  • Q & A
  • 5 min

Application procedure:

If you are interested in attending the workshop, please complete the questionnaire (just the items between the lines below) and send to Jianhong Ou, Ph.D. <jianhong.ou@duke.edu) by email by 5 pm on May 4, 2022.

Applicants will be notified of selection decision by May 6.

Please answer the following questions to best of your knowledge.

1. Are you comfortable using linux? If you have no linux experience please indicate that (prior experience is not required/expected).

2. Have you done QIIME2 analysis before? If yes, how comfortable are you with QIIME2 package?

3. Have you done any microbiome related data analysis before? If yes, can you summarize your experience?

4. Do you have your own microbiome/metagenome sequencing dataset you are planning to bring? (if yes, specify if 16S rRNA amplicon or WGS sequencing). If you presently don't have your own data are you planning to do a related experiment soon?

5. Provide some biographical information.

A. Your Information

Name:

Duke Email:

Duke Unique ID:

Contact phone:

Current Duke Affiliation (student, postdoc, staff, faculty):

B. Information about your PI (if you are not the PI)

Name:

Department:

Duke Email: