Environmental Genomics training course
23 - 25 October 2019
Gießen, GermanyEnvironmental Genomics training course https://www.denbi.de/training/700-environmental-genomics-training-course https://tess.elixir-europe.org/events/environmental-genomics-training-course 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 2019-10-23 09:00:00 UTC 2019-10-25 17:00:00 UTC de.NBI Gießen, Gießen, Germany Gießen Gießen Gießen Germany    workshops_and_courses  
6th de.NBI Genomics training course
4 - 6 May 2020
Gießen, Germany6th de.NBI Genomics training course https://www.denbi.de/training/814-6th-de-nbi-genomics-training-course https://tess.elixir-europe.org/events/6th-de-nbi-genomics-training-course Educators: Alexander Goesmann, Sven Griep, Oliver Rupp, Tobias Zimmermann, Oliver Schwengers, Andreas Hoek, Jochen Blom, Sebastian Jaenicke (BiGi) Date: 04.-06.05.2020 Location: Heinrich-Buff-Ring 58, Justus-Liebig-Universität, Gießen, Seminar Rm. 0024a Content: The first day will introduce software tools for the quality control of short read data. For conducting basic sequence read processing steps we will use our local Galaxy server. In the last session we will explain the basic approaches for genome assembly and run various genome assemblers: - Introduction to quality control - Automatic trimming of sequencing reads - The basics of genome assembly On the second day we will take a closer look at the genome assembly results. Afterwards, we provide a comprehensive introduction to microbial genome annotation. Available tools and algorithms for the different genome analysis and annotation steps will be explained and used within Galaxy. The GenDB genome annotation pipeline will be presented as well as a new stand-alone high-throughput genome analyses pipeline (ASA3P) that can be used to process thousands of genomes on a single day: - The basic principles of region and function annotation - Genome annotation tools and pipelines in Galaxy - Manual and distributed genome annotation using GenDB - Introduction to the ASA3P software 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 - Statistical analyses (core/pan/singleton development plots) - The public EDGAR database Agenda: Day 1: Quality control & genome assembly 13:00 – 13:15 Welcome & introduction (Alexander Goesmann) 13:15 – 13:30 Transfer of data sets 13:30 – 15:00 Read quality control & trimming incl. hands-on session (Sven Griep, Oliver Rupp) 15:00 – 15:30 Coffee Break 15:30 – 17:00 Introduction to genome assembly incl. hands-on session (Sven Griep, Oliver Rupp) Day 2: Microbial Genome Annotation 9:00 – 10:30 Introduction to microbial genome annotation (Alexander Goesmann) 10:30 – 11:00 Coffee Break 11:00 – 12:30 Genome annotation with Galaxy & GenDB hands-on session (Sven Griep, Oliver Rupp, Tobias Zimmermann) 12:30 – 13:30 Lunch 13:30 – 14:30 Introduction to ASA3P (Oliver Schwengers) 14:30 – 15:00 Coffee Break 15:00 – 17:00 ASA3P practical session (Oliver Schwengers, Andreas Hoek) 17:30 Optional: Tour to Gleiberg castle Day 3: Comparative Genomics 9:00 – 10:30 EDGAR (Jochen Blom) 10:30 – 11:00 Coffee Break 11:00 – 12:00 EDGAR hands-on (Jochen Blom, Sebastian Jaenicke) 12:00 – 12:30 Course evaluation & closing remarks (all hands) During the afternoon of the last day participants are invited to discuss open questions or individual projects or data sets with the course experts. Learning goals: On all three days the program includes extensive hands-on training to allow participants to get familiar with the presented software. Participants can bring their own datasets that fit the topics of the workshop. The data can be analyzed in the hands-on sessions. Prerequisites: None Keywords: Quality control, genome assembly, Microbial Genome Annotation, Comparative Genomics Tools: Galaxy, GenDB, ASA3P, EDGAR 2020-05-04 09:00:00 UTC 2020-05-06 17:00:00 UTC de.NBI Gießen, Gießen, Germany Gießen Gießen Gießen Germany    workshops_and_courses  
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