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Genomics and transcriptomics are rapidly becoming standard methods to examine living systems. This workshop provides an introduction to the methods and tools used to analyse next-generation-sequencing data, provides understanding of its limitations and a basic understanding on how the analysis algorithms work. This workshop will take the participants through an example project demonstrating how to evaluate the quality of data as provided by a sequencing facility, how to perform a de-novo genome assembly, and how to align the data against a known and annotated reference genome. Furthermore, participants will learn how to compare transcription data between different samples.

The workshop is scheduled for 18th - 22nd of August, from 9:30 to 17:00, and will consist of seminars intertwined with hands-on sessions and discussions. The course is open for all students, postdocs and research scientists of BESE division.

Major topics to be covered: Genome assembly, Transcriptomics, Visualization and Tips/tricks.

1. Introduction to programming basics
2. Utility commands in data management
3. Common file formats in NGS data
4. Introduction to High-Performance Computing environment

1. Introduction to Next-Generation-Sequencing
2. Quality control on raw data
3. Assembling a small genome sequence

3. Assembly QC
4. Annotating genes
5. Using long reads for assembly
6. Hybrid Assembly QC

1. Experimental design and strategies
2. Data cleaning + mapping
3. Quantification
4. Visualization

5. Differential expression
6. Functional annotation
7. Alternative splicing
8. Summary + QA + Recap

• Arun Nagarajan, PostDoc at KAUST, is interested in understanding the molecular mechanism of acclimatization to stress by a biological organism using new-age technology.
• Robert Lehmann, Research Scientist at KAUST, integrates genetic and transcriptomic data to gain insights into genetic responses to stress in established model organisms as well as new marine model organisms.
• Octavio Salazar Moya, PostDoc at KAUST, is interested in increasing food production, particularly by increasing salt tolerance of plants.
• Manjula Thimma, Research Scientist at KAUST, is interested in understanding the role of retrotransposons in cell identity, reprogramming and differentiation.
• Alaguraj Veluchamy, Research Scientist at KAUST, is interested in TBA

TBA

• Arun Nagarajan
• Manjula Thimma
• Robert Lehmann