Alexander Goesmann, Jochen Blom, Oliver Rupp, Oliver Schwengers (BiGi)
07.06.2017 – 09.06.2017
Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, Room 0024a
Topic of this three-day-workshop will be sequence data analysis including quality control, assembly, genome annotation and comparative genomics with a focus on the usage of the BiGi software tools ASA3P and EDGAR as well as the BIGI Galaxy Server.
The first day will give a comprehensive introduction to the primary data management in sequencing projects. In this part tools for sequence analysis available via the Galaxy-Server of BIGI will be in the focus of the workshop.
- Initial quality assessment and quality control of raw sequencing data
- Data preparation, filtering and quality trimming
- Assembly strategies for different datasets
The second day will provide an overview of microbial genome annotation. The basic principles of regional and functional annotation will be introduced, and available tools and algorithms for the different annotation steps will be explained. The ASA3P platform for high-throughput parallel genome annotation and its capabilities in antibiotic resistance and virulence factor detection will be presented in detail.
- The basic principles of regional and functional annotation
- Genome annotation pipelines for single and multiple genomes
- High throughput genome annotation using ASA3P
The third day will provide an introduction to 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 become familiar with the presented software.
Principles of computational sequence analysis, hands-on experience with de.NBI software services
Sequence data analysis, genomics, annotation, comparative genomics, phylogenetic analysis
GenDB, ASA3P, EDGAR, ReadXplorer, BLAST, HMMER, PHYLIP