Educators:
Alexander Goesmann, Jochen Blom, Oliver Rupp, Oliver Schwengers (BiGi)
Date:
21.09.2016 - 23.09.2016
Location:
Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, Room 0024a
Contents:
Topic of this three-day-workshop will be sequence analysis with a focus on short-read mapping data, genome annotation and comparative genomics with a focus on the usage of the BIGI software tools ReadXplorer, GenDB and EDGAR.
The first day will introduce the ReadXplorer software for the the analysis of short read mapping data:
- Handling of complex experimental settings in the ReadXplorer user interface
- Automatic analysis of re-sequencing experiments (SNP detection, coverage statistics, ...)
- Automatic interpretation of RNA-Seq experiments (differential gene expression, transcription start site detection, operon analyses, …)
The second day will give a comprehensive introduction into microbial genome annotation. Available tools and algorithms for the different annotation steps will be explained. The GenDB genome annotation pipeline will be presented as well as a new stand-alone high-throughput genome analyses pipeline:
- The basic principles of regional and functional annotation
- Genome annotation pipelines
- Manual and distributed genome annotation using GenDB
The third day will give an introduction into comparative genomics with a focus on differential gene content analysis using the EDGAR platform. The use of the BLAST score ratio values (SRVs) to measure the similarity between coding sequences and to assess orthology will be introduced. All features of EDGAR will be introduced in detail:
- Genomic subset calculations (core-genome, pan-genome, singleton genes)
- Core-genome-based phylogenetic analyses
- Sequence based phylogeny
- ANI, AAI, GGDC
- Statistical analyses (core/pan/singleton development plots)
- The public EDGAR database
On all three days the program includes extensive hands-on training to allow participants to get familiar with the presented software.
Learning goals:
Principles of computational sequence analysis, hands-on experience with de.NBI software services
Prerequisites:
-
Keywords:
Short-read mapping data analysis, genomics, annotation, comparative genomics, phylogenetic analysis,
Tools:
GenDB, ASA3P, EDGAR, ReadXplorer, BLAST, HMMER, PHYLIP
Contact:
We have to demand a 30 Euro fee to cover our expenses for catering, apart from that the workshop is free. For more information see:
https://www.uni-giessen.de/fbz/fb08/Inst/bioinformatik/Education/courses/content/course092016