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DTSTART;TZID=Europe/Stockholm:20231113T090000
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UID:153663-1699866000-1700240400@www.scilifelab.se
SUMMARY:Introduction to bioinformatics using NGS data
DESCRIPTION:National workshop for PhD students\, postdocs\, researchers\, and other employees within Swedish academia\, introducing the analysis of next generation sequencing data. \n\n\n\nThe course is organized by: National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI) \n\n\n\nResponsible teachers: Malin Larsson\, Martin Dahlö\, Roy Francis \n\n\n\nContact information: edu.intro-ngs@nbis.se  \n\n\n\n\n\n\n\n\n\nApply here\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Jun 7\, 2023 \n\n\n\nApplication deadline: October 4\, 2023 \n\n\n\nConfirmation to accepted participants: Week 41 (October 9-12) \n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis on-site training event costs 3000 SEK for academic participants\, invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced 3000 SEK. Please note that NBIS cannot invoice individuals. We ask non-academic applicants to contact us regarding the fee.  \n\n\n\n\n\n\n\nCourse description\n\n\n\nThis intense one-week workshop provides an introduction to the analysis of next generation sequencing data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform\, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures.  \n\n\n\n\n\n\n\nCourse content\n\n\n\nBriefly\, the workshop covers the followings major topics: \n\n\n\n\nWorking on the UNIX/LINUX command line\n\n\n\nBioinformatic/NGS data formats and QC\n\n\n\nDNA variant calling workflow essentials\n\n\n\nRNA sequence analysis workflow essentials\n\n\n\n\n\n\n\n\nLearning outcomes\n\n\n\nAfter this workshop you should be able to: \n\n\n\n\nDescribe the basic principles of next generation sequencing.\n\n\n\nUse the Linux command line interface to manage simple file processing operations\, and organise directory structures.\n\n\n\nConnect to and work on a remote high performance compute cluster.\n\n\n\nApply programs in Linux for analysis of NGS data.\n\n\n\nSummarise the applications of current NGS technologies\, including the weakness and strengths of the approaches and when it is appropriate to use which one of them.\n\n\n\nExplain common NGS file formats.\n\n\n\nInterpret quality control of NGS reads.\n\n\n\nExplain the steps involved in variant calling using whole genome sequencing data.\n\n\n\nIndependently perform a basic variant calling workflow on example data.\n\n\n\nDemonstrate hands-on experience with handling raw RNA sequencing data\, QC and quantification of gene expression.\n\n\n\nExplain the steps involved in differential gene expression using RNA seq data.\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nTo be able to follow the workshop you need to: \n\n\n\n\nBYOL\, bring your own laptop configured according to precourse instructions.\n\n\n\nHave a background in genetics\, cell biology\, biomedicine\, biochemistry\, bioinformatics or comparable.\n\n\n\nTo get the maximum benefit from the workshop you should:\n\n\n\nHave a research project where you are currently using or are planning to use next generation sequencing.\n\n\n\n\n\n\n\n\n\n\nSelection criteria\n\n\n\nDue to limited space the course can accommodate a maximum of 30 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers\, and we will prioritise applications  from Swedish academia.
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-3/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
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