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  • Monday, July 26, 2021
  • Wednesday, July 28, 2021

SC4ES: NCGAS Transcriptome Assembly, Annotation, and Analysis Workshop

The National Center for Genome Analysis Support (NCGAS) offers this three-day, online, semi-asyncrhonous workshop on high performance computing (HPC) usage and transcriptome assembly, annotation and analysis. Applications due June 13, 2021.

Event details

  • Date & time
    Monday, July 26, 2021
  • Location
    Online
  • Date & time
    Tuesday, July 27, 2021
  • Date & time
    Wednesday, July 28, 2021

Register here

About this event

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The National Center for Genome Analysis Support (Links to an external site.) (NCGAS) offers this three-day, online, semi-asyncrhonous workshop on high performance computing (HPC) usage and transcriptome assembly, annotation and analysis. The workshop consists of discussions, lectures, and hands-on tutorials/activities to cover topics important to getting started constructing and analyzing transcriptomes.  While the focus is largely on de novo assembly, genome-guided transcriptome assembly and analysis is discussed, and demo code is provided. Material covers both the availability and use of HPC resources, alongside the task of assembling a new transcriptome, in order to provide a more comprehensive preparation for this and future bioinformatic tasks. The main case study will consist of using four separate assemblers (Trinity, SOAP de novo, Velvet Oases, and TransABySS), with multiple kmers, to be combined and curated with Evigenes. This combined assembly with multiple parameters is considered much more robust than simply using one assembler, and the NCGAS pipeline streamlines the process and allows for customization if desired. Downstream analyses such as differential expression, generating KEGG pathway images, and annotation using Trinotate will also be discussed. 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 only—but you must register to be considered. Click on the registration button to apply - applications due by end of day, June 13, 2021.


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
  • How to run NCGAS’s transcriptome tools to produce robust transcriptomes
  • How to check quality and clean up a de novo transcriptome
  • Familiarity with some of the considerations in downstream analyses
  • How to get help for both genomic and computational questions

Participant data will not be assembled during the workshop, but the entire pipeline will be used by participants with smaller scale demo data. There will be a limited number of slots to meet with NCGAS personnel to discuss your data. Online meetings after the workshop can also be scheduled.


Prerequisites

This workshop is geared for beginners but basic Unix commands were not 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:


Agenda

Day 1:

  • Introduction to NCGAS staff
  • Introduction to clusters and usage
  • Optimizing jobs
  • Overview of de novo transcriptome analysis pipeline
  • Data management and movement tutorial
  • National HPC resource availability discussion

Day 2:

  • Introduction to the case study
  • Introduction to RNAseq data and considerations
  • QC of raw data
  • Using and troubleshooting the workflow
  • Annotation using Trinotate
  • Introduction to KEGG pathway analysis

Day 3:

  • Differential expression discussion and demo
  • Genome-guided analysis discussion and demo
  • Case study wrap up

The Supercomputing for Everyone Series (S4ES) of workshops and seminars are led by personnel from Research Technologies (Links to external site.), a division of University Information Technology Services (Links to external site.). This series is led by the National Center for Genome Analysis Support (Links to external site.). Both are centers in the Pervasive Technology Institute (Links to external site.) at Indiana University.

The Supercomputing for Everyone Series (Links to external site.) aims to bring more users into the realm of advanced computing, whether it be visualization, computation, analytics, storage, or any related discipline. Let the Research Technologies staff take you to the next level of computing.