8th Galaxy workshop on HTS data analysis
23 - 27 September 2019
Freiburg im Breisgau, Germany8th Galaxy workshop on HTS data analysis https://www.denbi.de/training/518-freiburg-galaxy-workshop https://tess.elixir-europe.org/events/8th-galaxy-workshop-on-hts-data-analysis Educators: RBC Freiburg Date: 23.-27.09.2019 Location: Uni Freiburg Contents: 1-week full-day hands-on workshop in Freiburg. Topics: - Galaxy Introduction - Data analysis of RNA-seq, ChIP-seq, Exome-seq, MethylC-seq data Learning goals: Using Galaxy for data analysis of HTS data. Topics: - Quality control - Mapping - Differential expression analysis - Workflow design - Statistics - Visualization. Prerequisites: No. Beginner training course! Keywords: Galaxy, NGS, HTS, RNA-seq, ChIP-seq, Exome-seq, MethylC-seq Tools: Galaxy 2019-09-23 09:00:00 UTC 2019-09-27 17:00:00 UTC de.NBI Freiburg im Breisgau, Freiburg im Breisgau, Germany Freiburg im Breisgau Freiburg im Breisgau Freiburg Germany    workshops_and_courses  
Galaxy for linking bisulfite sequencing with RNA sequencing
9 - 12 October 2019
Freiburg im Breisgau, GermanyGalaxy for linking bisulfite sequencing with RNA sequencing https://www.denbi.de/training/663-galaxy-for-linking-bisulfite-sequencing-with-rna-sequencing https://tess.elixir-europe.org/events/galaxy-for-linking-bisulfite-sequencing-with-rna-sequencing-7b7b1d40-b65b-4694-a5c7-9613dfb3e2c7 Educators: Konstantin Riege (Jena), Steve Hoffmann (Jena), Steffen C. Lott (Freiburg), Wolfgang Hess (Freiburg), Andrea Bagnacani (Rostock), Markus Wolfien (Rostock), Olaf Wolkenhauer (Rostock) (RBC / de.STAIR) Date: 9.-11.10.2019 Location: Albert-Ludwigs-Universität Freiburg, Schänzlestraße 1, 79104 Freiburg im Breisgau Contents: In this training course, we introduce the Galaxy framework (https://usegalaxy.eu) for biomedical data analyses, and showcase its tools for data handling and preprocessing, differential gene expression analysis, bisulfite sequencing analysis, and Oxford Nanopore data exploration and usage. Lectures will be provided on the topics of RNA and Bisulfite sequencing, Epigenetics, and basic statistics, and followed by hands-on sessions. Finally, we showcase a Galaxy Docker installation for customized workflow analysis. Learning goals: - Know your data, and the implications of data preprocessing and quality control - Performing differential gene expression analysis using Galaxy - Performing differential methylation analysis using Galaxy - Handling and analyze Oxford Nanopore sequencing data Prerequisites: This workshop is intended for MSc/PhD students, postdocs, and researchers with a background in Life Science research. During registration, please hand over a poster about a research topic of your choosing. Posters will be presented during our poster session, which you can use to exchange experiences with other participants. Keywords: Galaxy, Workflow development, Differential gene expressionanalysis, differential methylation analysis, Epigenetics, Oxford Nanopore Tools: Galaxy (https://usegalaxy.eu), Galaxy Training material (https://galaxyproject.github.io/training-material/) Contact: firstname.lastname@example.org Register: https://www.leibniz-fli.de/de/news-events/seminare/news-detailpage/news/denbidestair-training-course-galaxy-for-linking-bisulfite-sequencing-with-rna-sequencing-1/ 2019-10-09 09:00:00 UTC 2019-10-12 00:00:00 UTC de.NBI Freiburg im Breisgau, Freiburg im Breisgau, Germany Freiburg im Breisgau Freiburg im Breisgau Freiburg Germany  destair [at] leibniz-fli.de     
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  
9th Galaxy workshop on HTS data analysis
17 - 21 February 2020
Freiburg im Breisgau, Germany9th Galaxy workshop on HTS data analysis https://www.denbi.de/training/720-9th-galaxy-workshop-on-hts-data-analysis https://tess.elixir-europe.org/events/9th-galaxy-workshop-on-hts-data-analysis Educators: RBC Freiburg Date: 17.-21.02.2020 Location: Uni Freiburg Contents: 1-week full-day hands-on workshop in Freiburg. Topics: - Galaxy Introduction - Data analysis of RNA-seq, ChIP-seq, Exome-seq, MethylC-seq data Learning goals: Using Galaxy for data analysis of HTS data. Topics: - Quality control - Mapping - Differential expression analysis - Workflow design - Statistics - Visualization. Prerequisites: No. Beginner training course! Keywords: Galaxy, NGS, HTS, RNA-seq, ChIP-seq, Exome-seq, MethylC-seq Tools: Galaxy 2020-02-17 09:00:00 UTC 2020-02-21 17:00:00 UTC de.NBI Freiburg im Breisgau, Freiburg im Breisgau, Germany Freiburg im Breisgau Freiburg im Breisgau Freiburg Germany    workshops_and_courses  
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