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Icrisat

International Workshop on Next Generation Sequencing (NGS) Data Analysis

(21 – 23 July 2009)
Gcp
Next Generation Sequencing (NGS) technologies enable the resequencing of entire plant genomes or the sampling of entire transcriptomes more efficiently and economically and with greater depth than ever before (see Varshney et al. 2009, Trends in Biotechnology). Rather than sequencing individual genomes, now it is possible to sequence hundreds or even thousands of related genomes to sample genetic diversity within and between germplasm pools. Identifying and tracking genetic variation is now so efficient and precise that thousands of variants can be tracked within large populations. These NGS technologies have significant implications on crop breeding. However, optimization and availability of appropriate methodologies and tools to analyze, visualize and intrepret NGS data are still in their infancy. With an objective to help crop genetics and breeding community to utilize NGS data for crop improvement, Generation Challenge Programme and ICRISAT organized this workshop.
More than 30 scientists, including 13 scientists from other countries (USA, UK, France, Korea, Japan, Australia, Mexico and Philippines) participated in the workshop. The workshop had four technical sessions and two brainstorming sessions in which participants shared their experience/views on data generation and analysis by using NGS technologies for accelerating plant genome research to understand genome dynamics as well as to facilitate crop breeding.
With an objective to share the experience and views of experts in NGS data analysis, we are providing the presentations made at this workshop. While these presentations are made freely available to everyone, you are requested to seek permission of the respective presenter/speaker, in case you may be required to use some of slides/figures, etc. and a proper citation (In: International Workshop on Next Generation Sequencing (NGS) Data Analysis, 21 – 23 July 2009, ICRISAT, Hyderabad, AP, India) to be given.
For any further information please contact Rajeev K Varshney or B Manjula.
Technical Sessions and Presentations
Tuesday, 21 July 2009
Session: Introduction
Overview on NGS technologies and workshop Rajeev Varshney, ICRISAT, India
 
Session: Genomic Resources, Assembly and Visualization
Illumina paired read data for gene discovery and assembly David Edwards, UQ/ACPFG, Australia
Comparative genomics of plant pathogenic bacteria -- bioinformatics of Illumina sequence data David Studholme, TSL, UK
Genome sequencing, analysis, and applications at NCGR Jimmy Woodward, NCGR, USA
Analytical tools to analyse NGS transcriptomic data under the framework of ARCAD project Xavier Argout, CIRAD, France
GNPAnnot: a platform for structural and functional annotation Gaetan Droc, CIRAD, France
Problems and prospects of de novo sequencing using NGS technologies T R Sharma, NRCPB, India
 
Wednesday, 22 July 2009
Session: SNP Discovery
SNP discovery from 454 data David Edwards, UQ/ACPFG, Australia
Studies of population diversity in legumes From genomic to intragenic scales Jimmy Woodward, NCGR, USA
Polymorphism detection using high throughput sequencing at TSL Dan MacLean, TSL, UK
Approaches for SNP discovery from NGS data Vivek Thakur, ICRISAT, India
 
Session: Gene Expression  
NGS-based approaches for rice transcriptomics Tsuyoshi Tanaka, NIAS, Japan
Homoeolog-specific expression in soybean through Illumina RNA-sequencing Jimmy Woodward, NCGR, USA
Analysis of NGS data @ SCRI David Marshall, SCRI, UK
Transcriptome assembly, annotation and digital gene expression analysis Mehar Asif, NBRI, India
 
Session: Miscellaneous (De novo genome sequencing, Metagenomics)
Algorithms and software for assembling short sequence reads David Studholme, TSL, UK
Approaches to the assembly of complex plant genomes and metagenomics @ ACPFG David Edwards, UQ/ACPFG, Australia
The Genome sequence of Glycine soja: massive parallel short read sequencing approach Kyung Do Kim/Dong Hyun Kim, SNU, Republic of Korea
NGS data analysis pipeline @ ICRISAT R Pradeep, ICRISAT, India
 
Thursday, 23 July 2009
Session: Costs, Outsourcing, Data Management
General overview (and experience of SCRI) on outsourcing and data management Dave Marshall, SCRI, UK
Experiences of ACPFG with data service providers and management of NGS data Dave Edwards, UQ/ACPFG, Australia
Experiences of TSL on NGS data management Dan MacLean, TSL, UK
Experimental design to maximize utility with NGS technologies Jimmy Woodward, NCGR, USA
Management of NGS data @IRRI Ramil Mauleon, IRRI, Philippines
Please contact : Dr Rajeev Varshney, Director-Center of Excellence in Genomics, ICRISAT, Patancheru, 502 324, India;
Office: +91 40 3071 3305; Email : r.k.varshney@cgiar.org
© Center of Excellence in Genomics. 2008