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  • de.NBI - CeBiTec Nanopore Workshop 2020 - Best Practice and SARS-CoV-2 applications

    30 November - 4 December 2020

    de.NBI - CeBiTec Nanopore Workshop 2020 - Best Practice and SARS-CoV-2 applications Educators: Stefan Albaum, Jan-Simon Baasner, Sebastian Jünemann, Nils Kleinbölting, Alexander Sczyrba, Alex Walender (BiGi), Daniel Wibberg (CAU), David Brandt, Christian Rückert, Jörn Kalinowski (CeBiTec) Date: 30 November – 4 December 2020 Location: Online Content: Aim of this workshop is to familiarize the participants with the Nanopore sequencing technology, its applications, the "Best Practice" bioinformatics workflows and the analysis of SARS-CoV-2 genomes. The Nanopore technology has greatly facilitated the assembly of prokaryotic, viral and eukaryotic genomes. Therefore, the workshop is focused on the establishment of finalized genome sequences, ranging from basecalling, quality assessment over assembly to sequence polishing and finally assembly evaluation. A focus in this years workshop is on the analysis of Nanopore sequenced SARS-CoV-2 genomes and a suitable workflow for resequencing based on the ARTIC bioinformatics protocol. The course will start with a one day webinar on best practices for the lab work on sequencing SARS-CoV2 and a “guided tour” showing the necessary bioinformatics steps. This part of the workshop is open to a large number of applicants. The following 4 days will be a mixture of talks and practical sessions in the de.NBI cloud introducing, in more detail, the Nanopore sequencing technology and bioinformatics processing tools, as, for instance, base calling, assembly and polishing.This part of the workshop is, however, limited to a smaller number of applicants. Learning goals: This workshop aims to teach basic skills and best practices to researchers working with Nanopore data, e.g. SARS-CoV-2. The full course will include all necessary steps from raw sequencing data to finalized genomes (1) with a de novo assembly and (2) with re-sequencing and mapping to a reference. Prerequisites: This workshop is intended for PhD students and postdocs with molecular biology background in genomics or SARS-CoV2 background. Good understanding of command line tools is a plus, but not required. Tools: minimap2, canu, pilon, guppy, porechop, medaka, poretools, nextstrain, quast, ARTIC pipeline Keywords: Nanopore sequencing, genome assembly, genomics, SARS-CoV2, 2020-11-30 09:00:00 UTC 2020-12-04 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • Data visualization using R

    7 December 2020

    Data visualization using R Educators: Markus Stepath, Karin Schork, Nils Hoffmann (BioInfra.Prot / LIFS) Date: Monday, 7th Dec 2020 Location: Online training Contents: In this course you will learn how to use the ggplot2 package in R to create informative and beautiful figures to communicate your omics data and analysis results. We will cover the following topics: - Usage of the tidyverse for data preprocessing - Usage of the ggplot2 R package - Presentation of different types of graphics and when to use them - Customization of graphics Please be aware that basic knowledge of R is taught in our course “Differential analysis of quantitative proteomics data” on Monday, 2nd Nov 2020 ( Learning goals: - Using the ggplot2 R package to create graphics for omics data - Decide which type of graph is appropriate for the given data - Ability to costumize the graphics using ggplot2 Prerequisites: - Basic understanding of high-dimensional data sets from quantitative proteomics or other life sciences; - Basic knowledge of R (e.g. data import, basic plots. This can for example be gained from our course “Differential analysis of quantitative proteomics data” (Monday, 2nd Nov 2020, - Computer with stable internet connection, headset and camera Keywords: R; tidyverse; ggplot2; high-throughput data; omics; proteomics; data analysis, graphics, data preprocessing Tools: Download and more information on R here: We recommend using an editor such as RStudio, see 2020-12-07 09:00:00 UTC 2020-12-07 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []

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