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  • Monday, October 7, 2019
  • Wednesday, October 9, 2019

S4ES: Metagenomic Analysis workshop

The National Center for Genome Analysis Support (NCGAS) offers this inagural three-day workshop on HPC usage and metagenomic analysis.

Event details

  • Date & time
    Monday, October 7, 2019
    8am-5:30pm
  • Location
    IU - Bloomington
  • Date & time
    Tuesday, October 8, 2019
    8am-5:30pm
  • Location
    IU - Bloomington
  • Date & time
    Wednesday, October 9, 2019
    8am-1pm
  • Location
    IU - Bloomington
  • Deadline
    August 15, 2019

Register here

About this event

The National Center for Genome Analysis Support, or NCGAS, at Indiana University is offering a National Science Foundation-sponsored, three-day workshop on High Performance Computing (HPC) usage and metagenomic analysis.  Registration is free, but application is required.

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 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, which 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 pre-register to be considered. Participation is limited mainly 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.

Beginner tutorials in Linux (bash) can be found here:

Getting Started on Unix Walkthrough (PDF)

Code Academy

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, 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: 8am-5pm

  • NCGAS staff introductions
  • Introduction to clusters and usage
  • Optimizing job submission
  • Data center tour
  • Data management and movement
  • Overview of metagenomics data collection

Day 2: 9am-5pm

  • Quality control and pre-assessment of the data
  • Introduction to metagenome assembly and assembly statistics
  • Installing programs locally
  • Assembling metagenome assembled genomes and quality assessment
  • Taxa and function identification
  • Downstream analysis

Day 3: 9am-1pm

  • Adding more datasets from SRA
  • Visualization using R

Use the registration link to start the application process.

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1-NCGAS-Workshop.JPG

de novo assembly of transcriptomes using HPC resources workshop
participants and instructors at Indiana University, April 30-May 1, 2018

 

Supercomputing for Everyone superheroes RT-Education Outreach and Training