Workshop
High-performance computing (HPC)

Date & Time (GMT+7) : November 5, 2022 | 11:00 - 16:30

Registration click
15 Slides

19th International Symposium on Rice Functional Genomics (SRFG) 2022 November 4-7, 2022

Workshop: Accelerated Workflow and Software Tools for Plant Genomes: Data processing from Raw data to Variants


 

Abstract :

The objective of this proposed workshop is to discuss an automation and acceleration of variant calling workflow at high-performance computing (HPC) platform for rice and other crop genomes. The workflow is designed for HPC platform, where the variants of 3,000 rice samples could be processed in less than one week, and the workflow is also suitable for other different system architectures that includes cluster (or cloud platform), and high-end workstations. During this workshop, we will demonstrate the example datasets from Rice, Maize, and Soybean. We classified the workflow into 4 Phases: (1) Genome mapping, (2) Variants discovery, (3) Call set refinement and combining variants, and (4) Variants matrixes. We are using Genome Analysis Toolkit (GATK) best practices for large-scale variants discovery and customized algorithm for data parallelization. We built every stage of this workflow is independent & flexible entity, where it can be seamlessly executed across different system architectures. The automation on every stage of the workflow is scalable across multiple nodes via data parallelization algorithm which will take care of data distribution. We developed a novel data parallelization algorithm, which takes care of chromosome splitting into multiple chunks, and it can be executed independently across the nodes to reduce the execution time. The flexibility of the workflow offers collaboration in data sharing, data processing (e.g., various stages based on their computational limitations), improve the resource utilization (e.g., simultaneously use different system architectures), minimize overall execution time and many more.


Objective:

  • Accelerating the variant calling workflow on HPC and cluster platform
  • Discuss the various Bioinformatics tools used in the workflow
  • Best performance tuning methods
  • Job dependency and example of workflow creation
  • Demos in every stage of the workflow
  • Workflow automation
  • Visualization of processed dataset

Prerequisite:

  • Basic Linux/UNIX skills,
  • Basic knowledge in Slurm schedulers,
  • Basic understanding in BWA, Samtools and GATK

Expectation from the workshop:

  • Design of an automated variant calling workflow
  • Optimal number of CPUs for rice variant calling workflow.
  • Example job script files (e.g., end-to-end rice variant workflow)
  • Demos
 


Agenda:

Sl. No.

Details

Speaker

Duration

Overview of KAUST Rice genome project and data processing

1.

Opening Remarks & Keynote

Prof. Rod A Wing

15 Min

2.

KAUST Computational Resources

Dr. Saber Feki

15 Min

3.

Overview of 3k Rice Genome project

Dr. Yong Zhou

10 Min

4.

Overview of Accelerated workflow for variant discovery

Dr. Nagarajan Kathiresan

10 Min

Coffee break 10 Min

Accelerated workflow for data processing and demos

1.

Tools for data preprocessing and demo (Phase #1)

Dr. Nagarajan Kathiresan
(workflow discussion and demos)

Dr. Yong Zhou
(Scientific discussion & support)

30 Min

Coffee break 10 Min

2.

Tools for Variant discovery and demo (Phase #2)

30 Min

Coffee break 10 Min

3.

Data parallelization methods, call set refinement and demo (Phase #3)

50 Min

Coffee break 10 Min

4.

Variant tables and demo (Phase #4)

30 Min

5.

Open discussion and feedback

10 Min




 

Registration click or Scan QR Code


ISRFG 2022
Le Méridien Phuket Beach Resort
November 4-7, 2022 | Phuket, Thailand.





































Login



Contact us

  • support@isrfg2022.org
  • isrfg2022@gmail.com
19th International Symposium on Rice Functional Genomics
November 4-7, 2022 | Phuket, THAILAND.
at Le Méridien Phuket Beach Resort
29 Soi Karon Nui, Karon, Muang, Phuket 83100 | Hotel Tel. (+66)76 370 100

Host Organization
Rice Science Center, Kasetsart Univesity
No. 1 Village No. 6 Kamphaeng Saen, Nakhon Pathom, 73140
Tel. (+66)34 355 192

ISRFG 2022
ISRFG 2022