dturaev / metagenomic-analysis-workshop

The National Center for Genome Analysis Support (NCGAS) offers a three-day workshop on High Performance Computing (HPC) usage and metagenomic analysis between October 7th to 9th, 2019.

Metagenomic analysis workshop Fall 2019

The National Center for Genome Analysis Support (NCGAS) offers a three-day workshop on High Performance Computing (HPC) usage and metagenomic analysis

Dates – Oct 7th to 9th, 2019
Location – Bloomington, IN
Registration – Closed / Deadline to apply - August 15th, 2019

Workshop Information

The workshop consists of discussions, lectures and hands-on tutorials, to cover topics important to constructing and analyzing metagenomic datasets. Material covers availability of HPC resources, and how to access these resources, while learning how to assemble and annotate metagenomics datasets. The goal of this workshop is to provide a comprehensive preparation for metagenomic analysis and other bioinformatic tasks. Metagenomic analysis will consist of learning how to the programs locally, assemble, and annotate the datasets to identify taxa and function. This workshop will walk through the general steps taken in most metagenomics studies. In addition, we will discuss other resources that support further downstream analysis to answer various research questions. While material will make heavy use of XSEDE and IU machines, the material is transferable to any cluster. Participation in this workshop is by invitation—you must register to be considered. Participation is limited by facility space.

Prerequisites

This workshop is geared for beginners, but basic Unix commands will not be covered. As such, participants must have basic Linux functionality (sign in, moving around file system, etc.), but expertise is not required. It would be helpful if participants had some exposure to using a cluster for compute jobs and an idea of the end goals for their data.

If you are working on a Windows machine, make sure to have Putty (https://www.putty.org/), or have Bash Desktop app.

Beginner tutorials in Linux (bash) can be found here:
Getting Started on Unix Walkthrough (pdf) (http://pages.iu.edu/~ss93/tutorials/GettingStartedonUnixWalkthrough.pdf)
Code Academy (https://www.codecademy.com/catalog/subject/all)

Objectives

Participants should leave with the following knowledge:

• Familiarity with nationally available compute resources
• An understanding of the differences, pros, and cons of VMs, Gateways, Clusters, and Clouds
• How to run and optimize a job submission on a cluster
• How to manage large data sets and move data between resources
• Basic steps in software installation and how to reach out for help when running into errors
• How to run metagenomics assembly and annotation
• Ability to reconstruct metagenome assembled genomes and check their quality
• How to get help for both genomic and computational questions

Participant data will not be analyzed during the workshop (that takes more time than we have!), but the entire pipeline will be used by participants with smaller scale demo data. We can also schedule online meetings after the workshop to discuss your data.

Schedule

Day 1	Activity	Lead
8:30am	Registration	All
9:00am	Introduction to NCGAS and staff	Tom
9:30am	Introduction to Clusters and Other Resources	Sheri
11:00am	BREAK
11:15am	Job submission	Carrie
12:15pm	Data Center Tour/Lunch
2:00pm	Data Management and Movement	Sheri
3:30pm	BREAK
3:45pm	Overview of metagenomics data	Tom
4:30pm	National Computing resources and support	Phil
5:30pm	BREAK
5:45pm	Publicly Available Resources	All
6:30pm	We will have reservations at a local tavern, Nick's. We will be joining you to chat/relax, but you will be responsible for paying for your meal and drinks.
Day 2	Activity	Lead
9:00am	Quality control and pre-assessment of data	Bhavya
10:45am	BREAK
11:00am	Hands on -Metagenome assembly and assembly stats	Bhavya
12:30am	Lunch
1:30pm	Software installation	Carrie
2:30pm	BREAK
2:45pm	Hands on- Metagenome assembled genomes and quality assessment	Bhavya
4:00pm	BREAK
4:15pm	Downstream analysis Discussion	Bhavya
6:00pm	We will meet at a favorite local bar, the Upstairs. They do not serve food, but there is plenty of food nearby that you can bring with you! Again, we will be joining you to chat/relax, but you will be responsible for paying for your meal and drinks.
Day 3	Activity	Lead
9:00am	Mining SRA pipeline	Bhavya
10:30am	BREAK
10:45am	Ordination plots in R	Sheri
12:30pm	BREAK
12:45pm	Final Remarks	Tom
1:00pm	Lunch: On your own, there are a couple restaurants nearby you can check out. A few of them are listed in the Welcome document given during registration

Presentations

Link to the presentations from workshop https://iu.box.com/s/ntfcr61kqrv4m74uwitk7a7i2bdzwlg3

Contact us

If you have any questions, email us at [email protected].
Website https://ncgas.org/
Twitter - @ncgas
Facebook - @ncgasiu