BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260807T062942Z UID:fb7ee3c5-7411-4baf-a235-2a067db1c9f8 DTSTART:20170403T060000Z DTEND:20170406T140000Z DESCRIPTION:Description\n\nMetagenomics investigates the composition and fu nction of microbial communities in different environments based on direct isolation of genetic material. It has been accelerated by the advances i n high-throughput sequencing technologies\, and the increasing data sizes require efficient analysis methods and advanced computing approaches.\n\nT his international workshop covers metagenomics analysis from quality cont rol\, filtering and assembly to taxonomic classification\, functional assi gnment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data\, the workshop has also an option al day on community analysis of amplicon sequencing data. Finally\, inter national databases and standards for storing the data are introduced.\n\nT he workshop consists of lectures and hands-on exercises. User-friendly ana lysis platforms META-pipe and Chipster are used in the exercises\, so no p rogramming skills are required\, and the workshop is thus suitable for eve rybody. \n\nMETA-pipe has been developed by ELIXIR-Norway\, and it offers tools for pre-processing (Prinseq\, FastQC)\, assembly (MetaRay/Ray\, Mir a)\, taxonomic classification (LC-classifier)\, gene prediction (Glimmer/M GA)\, functional analysis (Blast\, Priam\, InterProScan) and visualizatio n (Metarep). META-pipe analysis jobs use a Spark cluster in the cloud for computation.\n Chipster offers over 360 analysis tools for different kind s of high-thoughput data. For community analysis of amplicon sequencing da ta it has tools for pre-processing (Prinseq\, Trimmomatic\, FastQC\, Mothu r)\, taxonomic classification (Mothur)\, and statistical analysis for mark er gene studies (R packages vegan\, rich\, biodiversityR\, pegas and labds v). \nThe workshop is organized in collaboration with the ELIXIR EXCELERA TE project.\n\nLecturers\n\nNils Willassen (ELIXIR-Norway)\n Espen Roberts en (ELIXIR-Norway)\n Erik Hjerde (ELIXIR-Norway)\n Aleksandr Agafonov (ELI XIR-Norway)\n Anu Mikkonen (University of Jyväskylä)\n Jenni Hultman (Un iversity of Helsinki)\n Petri Auvinen (University of Helsinki)\n Jarno Tui mala (RS training)\n Maria Lehtivaara (CSC)\n Kimmo Mattila (CSC)\n Eija K orpelainen (CSC)\nProgram\n\nPlease note that there might be still small c hanges to the schedule.\n\nDay 1\, Monday 3.4.2017: OPTIONAL MODULE - Com munity analysis of amplicon sequencing data\n\n9:00-10:45 LECTURES\n\nWho 's there? Community analysis by amplicon sequencing (Anu Mikkonen)\n Short demo: Using QIIME in parallel fashion in HPC environments (Kimmo Mattila) \n10:45-11:00 Coffee break\n\n11:00-12:30 HANDS-ON SESSION: Using the Chi pster software to analyze 16S rRNA data (Eija Korpelainen\, Maria Lehtiv aara\, Anu Mikkonen)\n\nIntroduction to Chipster\n Data preprocessing with Mothur-based tools and FastQC\n12:30-13:30 Lunch\n\n13:30-16:30 HANDS-ON SESSION: Using Chipster continues (Eija Korpelainen\, Maria Lehtivaara\ , Anu Mikkonen and Jarno Tuimala) // coffee break included\n\nData preproc essing with Mothur-based tools\n Taxonomic classification with Mothur-base d tools\n Statistical analysis of marker gene data: Comparing diversity an d abundance between groups\n Visualization\nDay 2\, Tuesday 4.4.2017: Samp le preparation\, sequencing\, quality control\, filtering and assembly\n\ n9:00-12:30 LECTURES\n\n\n 9:00-10:15 Selecting and preparing samples for metaomics (Anu Mikkonen)\n\n Your samples are only as good as your sample preparation routines are\, and your results are only as valid as your exp erimental design is. This talk will discuss\, showing plenty of real-life examples\, all the things that can go wrong before you even send your DNA samples out for the sequencing. The talk includes lots of practical recom mendations on what to do before\, or sometimes instead of\, metagenomics a nalysis.\n \n \n 10:15-10:45 Sequencing technologies for metagenomics (Pe tri Auvinen)\n \n10:45-11:00 Coffee break\n\n\n 11:00-11:30 Metagenomics analysis – an overview (Nils Willassen)\n \n \n 11:30-12:00 META-pipe analysis platform overview (Espen Robertsen\, Erik Hjerde)\n \n \n 12:00-1 2:30 Metagenomics in the cloud (Aleksandr Agafonov)\n \n12:30-13:15 Lunc h\n\n13:15-16:30 HANDS-ON EXERCISES: Using the META-pipe platform (Nils Wi llassen\, Espen Robertsen\, Erik Hjerde) / / coffee break included\n\nQual ity control and filtering\n Assembly\n Validation\nDay 3\, Wednesday 5.4.2 017: Taxonomic and functional analysis\n\n9:00-11:30 LECTURES\n\n9:00-9:30 Taxonomic classification (Nils Willassen)\n 9:30-10:00 Functional assignm ent (Espen Robertsen)\n10:00-10:15 Coffee break\n\n10:15-10:45 New data resources for marine metagenomics (Nils Willassen)\n 10:45-11:15 The meta genomics data life-cycle: standards and best practice (TBD)\n11:15-12:00 H ANDS-ON EXERCISES: Using the META-pipe platform (Nils Willassen\, Espen R obertsen\, Erik Hjerde)\n\nIntroduction\, taxonomic classification\n12:00- 13:00 Lunch\n\n13:00-16:30 HANDS-ON EXERCISES: Using the META-pipe platfor m continued (Nils Willassen\, Espen Robertsen\, Erik Hjerde) / / coffee br eak included\n\nTaxonomic classification continued\n Functional assignment \nDay 4\, Thursday 6.4.2017: Comparative metagenomics and other analysis\n \n9:00-12:00 HANDS-ON EXERCISES: Using the META-pipe platform continued (N ils Willassen\, Espen Robertsen\, Erik Hjerde) / / coffee break included\n \nVisualization of data\n Comparative metagenomics\n12:00-13:00 Lunch\n\n1 3:00-14:30 LECTURES AND WRAP-UP\n\n13:00-13:35 Arctic metagenomes as a sc affold for understanding metatranscriptomic data (Jenni Hultman)\n 13:35- 14:00 Genome assembly from metagenomic reads (Jenni Hultman)\n 14:00-14:3 0 Feedback and wrap up\n \n\nLanguage:  EnglishPrice:          Free of charge\n\nhttps://events.prace-ri.eu/event/602/ LOCATION:CSC Finland Oy SUMMARY:Metagenomics Data Analysis Workshop @ CSC URL;VALUE=URI:https://www.csc.fi/web/training/-/metagenomics END:VEVENT END:VCALENDAR