Educators:
Jochen Blom, Oliver Rupp, Oliver Schwengers, Sebastian Jaenicke (BiGi), Stefanie Glaeser

Date:
23.10.2019 – 25.10.2019

Location:
Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, Room 0024a

Contents:
Topic of this three-day-workshop will be sequence data analysis including quality control, assembly, genome annotation and comparative genomics with a focus on microbial taxonomy and phylogenomics and as the usage of the BiGi software tools ASA3P, EDGAR, and MGX.

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

Furthermore, 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 second day will provide an introduction to the role of genotypic methods in prokaryotic taxonomy including the 16S rRNA gene sequence phylogeny and genome sequences in the identification of environmental isolates. It will will also demonstrate the use of genome sequences to explore the functions of those isolates.

• The basic role of 16S rRNA gene sequences in Prokaryotic identification in taxonomic and ecology
• Concept of the phylogenetic analysis of environmental 16S rRNA gene amplicon datasets (introduction of SilvaNGS)
• Current role of genome sequences in species identification

Subsequently the EDGAR platform for comparative genomics will be introduced. One main topic will be its use for phylogenetic analyses based on genome similarity indices and the complete core genome of organisms. All features of EDGAR will be introduced in detail.
• Genomic subset calculations (core-genome, pan-genome, singleton genes)
• Core-genome-based phylogenetic analyses
• Core genome based phylogeny
◦ ANI, AAI, GGDC
• Statistical analyses (core/pan/singleton development plots)
• The public EDGAR database

The third day will show solutions for whole genome shotgun metagenomics. mWGS metagenomics has the potential to address the full spectra of genome-based issues. The focus here will be on taxonomic and functional analysis with the aid of different bioinformatic tools. The software solution MGX, an integrated platform for metagenome analysis and data visualization, will be demonstrated as comprehensive platform for read-based metagenome analysis.
• The basic principles of metagenome analysis
• Available pipelines for taxonomic and functional analysis
• Statistical features: PCA, PCoA, Rarefaction, …

The afternoon of the third day will be kept free for custom data analysis consulting. Participants are encouraged to bring their own data which can be discussed with the bioinformatics experts of the Bielefeld-Gießen Resource Center for Microbial Bioinformatics (BiGi).

On all three days the program includes extensive hands-on training to allow participants to become familiar with the presented software.

Learning goals:
Principles of computational sequence analysis, hands-on experience with de.NBI software services

Prerequisites:
None

Keywords:
Sequence data analysis, genomics, annotation, comparative genomics, phylogenetic analysis, metagenome analysis

Tools:
GenDB, ASA3P, EDGAR, MGX