Plant Bioinformatics - 'Genomic & transcriptomic Analysis'

5-7 September 2016

Prof. Chris Kuhlemeier, University of Bern; Rémy Bruggmann, SIB, University of Bern.

Prof. Aureliano Bombarely, Virginia Tech University

Assistants : Moser Michel, UNIBE; T.b.a.

The classes will be organized for 3 days, 2 hours for lectures during the morning and exercises for the afternoon.

The following topics will be covered :

- Next Generation Sequencing and Read Processing

Describtion of the different Next Generation Sequencing (NGS) technologies, library preparations and types, sequencing quality evaluation and read preprocessing. Terms such as mate pair, pair end, multiplexing, qscore, fastq should be familiar at the end of the class. The practice will be based in the read processing and read quality evaluation. Two different datasets will be used for this purpose (gDNA and cDNA reads). Basic Linux knowledge will be required to run the commands.

- Sequence Assembly

Brief summary of the history of the genome assembly as introduction. It will be followed by the different assembly strategies and tools that are commonly used and the methods to evaluate the quality of the assembly. Some of the most common problems for the assembly of the complex genomes will be discussed. The last part of the lecture will be focused in the transcriptome assembly. The practical part of the class will be the assembly of the N. benthamiana chloroplast genome with different datasets and conditions.

- Sequence Annotation

Presentation of the different methodologies to predict gene models (ab-initio and evidence based). The most used methodologies and the most common error sources will be discussed. Additionally a brief introduction repeat analysis will complete the landscape for the genome structural annotation. For other hand the functional gene annotation will be summarized. Finally the most common gene annotation formats such as GFF or GTF will be presented. The practice will be focused in a small genome annotation, comparison between different ab-initio and evidence based tools and the discussion of the possible source or error.

Université de Berne

Please contact Prof. Chris Kuhlemeier at [email protected] .

Priority is given to CUSO students till June 30.

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