Metagenomics Analysis

The National Center for Genome Analysis Support (Links to an external site.) (NCGAS) provides this workshop which includes discussions, lectures, and hands-on tutorials to cover topics important to constructing and analyzing shotgun sequenced metagenomic datasets.

Material covers availability of HPC resources, 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. While the material makes heavy use of XSEDE and IU machines, the material is transferable to any cluster.

The NCGAS was funded by the National Science Foundation under Grant Nos. DBI-1062432 2011 , ABI-1458641 2015 , and ABI-1759906 2018 to Indiana University.

Learning Objectives

By the end of this workshop, 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
Quality control of data
How to run metagenomics assembly
Ability to reconstruct metagenome assembled genomes and check their quality
Taxa and functional annotation of metagenomes
How to get help for both genomic and computational questions

Prerequisite Skills

Basic Linux functionality (sign in, moving around file system, etc.), but expertise is not required. Take the Unix the Basics course.
For online courses, you will need your own computer and access to the internet
- An SSH client is required. This knowledge base article is helpful: https://kb.iu.edu/d/ahjh (Links to an external site.)
- Mac and Linux machines should have built in SSH clients. For Windows, check and see if you have a program called PuTTY. If you have Windows 10, you may also consider installing the Windows subsystem for Linux: https://docs.microsoft.com/en-us/windows/wsl/install-win10 (Links to an external site.)

For in-person workshops, a laptop is required—if you do not have one, contact the organizer to borrow one

Agenda

Introduction to HPC and nationally available resources
Job submission on HPC resources
Overview of metagenomics data
Metagenome assembly and quality assessment
Metagenome assembled genomes and quality assessment
Taxa and functional annotation
Downstream analysis

Access the course materials

Metagenomics Analysis (on GitHub)

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Supercomputing for Everyone Series workshops and seminars are led by personnel from Research Technologies, a division of University Information Technology Services and a center in the Pervasive Technology Institute at Indiana University.

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