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DTSTAMP:20260708T112235Z
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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	Inge Alexander Raknes (
 ELIXIR-Norway)\n	Rob Finn (EBI)\n	Anu Mikkonen (University of Jyväskylä)
 \n	Jenni Hultman (University of Helsinki)\n	Petri Auvinen (University of H
 elsinki)\n	Jarno Tuimala (RS training)\n	Maria Lehtivaara (CSC)\n	Kimmo Ma
 ttila (CSC)\n	Eija Korpelainen (CSC)\nProgram\n\nPlease note that there mi
 ght be still small changes to the schedule.\n\nDay 1\, Monday 3.4.2017: O
 PTIONAL MODULE - Community analysis of amplicon sequencing data\n\n9:00-10
 :45 LECTURES\n\nWho's there? Community analysis by amplicon sequencing (A
 nu Mikkonen)\n	Short demo: Using QIIME in parallel fashion in HPC environm
 ents (Kimmo Mattila)\n10:45-11:00 Coffee break\n\n11:00-12:30 HANDS-ON SE
 SSION: Using the Chipster software to analyze 16S rRNA data (Eija Korpel
 ainen\, Maria Lehtivaara\, Anu Mikkonen)\n\nIntroduction to Chipster\n	Dat
 a preprocessing with Mothur-based tools and FastQC\n12:30-13:30 Lunch\n\n1
 3:30-16:30 HANDS-ON SESSION: Using Chipster continues (Eija Korpelainen
 \, Maria Lehtivaara\, Anu Mikkonen and Jarno Tuimala) // coffee break incl
 uded\n\nData preprocessing with Mothur-based tools\n	Taxonomic classificat
 ion with Mothur-based tools\n	Statistical analysis of marker gene data: Co
 mparing diversity and abundance between groups\n	Visualization\nDay 2\, Tu
 esday 4.4.2017: Sample preparation\, sequencing\, quality control\, filter
 ing and assembly\n\n9:00-12:30 LECTURES\n\n\n	9:00-10:15 Selecting and p
 reparing 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 experimental design is. This talk will discuss\, showing
  plenty of real-life examples\, all the things that can go wrong before yo
 u even send your DNA samples out for the sequencing. The talk includes lot
 s of practical recommendations on what to do before\, or sometimes instead
  of\, metagenomics analysis.\n	\n	\n	10:15-10:45 Sequencing technologies 
 for metagenomics (Petri 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 Hje
 rde)\n	\n	\n	12:00-12:30 Metagenomics in the cloud (TBD)\n	\n12:30-13:15
  Lunch\n\n13:15-16:30 HANDS-ON EXERCISES: Using the META-pipe platform (N
 ils Willassen\, Espen Robertsen\, Erik Hjerde) / / coffee break included\n
 \nQuality control and filtering\n	Assembly\n	Validation\nDay 3\, Wednesday
  5.4.2017: Taxonomic and functional analysis\n\n9:00-11:30 LECTURES\n\n9:0
 0-9:30 Providing the generalist EBI metagenomics platform: challenges and 
 issues (Rob Finn) \n	9:30-9:50 The metagenomics data life-cycle: standar
 ds and best practice (Rob Finn)\n	9:50-10:20 New data resources for marin
 e metagenomics (Nils Willassen)\n10:20-10:35 Coffee break\n\n10:35-11:15 
 Taxonomic classification and functional assignment (Espen Robertsen\, Erik
  Hjerde)\n11:15-12:00 HANDS-ON EXERCISES: Using the META-pipe platform (N
 ils Willassen\, Espen Robertsen\, Erik Hjerde)\n\nIntroduction\, taxonomic
  classification\n12:00-13:00 Lunch\n\n13:00-16:30 HANDS-ON EXERCISES: Usin
 g the META-pipe platform continued (Nils Willassen\, Espen Robertsen\, Eri
 k Hjerde) / / coffee break included\n\nTaxonomic classification continued\
 n	Functional assignment\nDay 4\, Thursday 6.4.2017: Comparative metagenomi
 cs and other analysis\n\n9:00-12:00 HANDS-ON EXERCISES: Using the META-pip
 e platform continued (Nils Willassen\, Espen Robertsen\, Erik Hjerde) / / 
 coffee break included\n\nVisualization of data\n	Comparative metagenomics\
 n12:00-13:00 Lunch\n\n13:00-14:30 LECTURES AND WRAP-UP\n\n13:00-13:35 Arc
 tic metagenomes as a scaffold for understanding metatranscriptomic data (
 Jenni Hultman)\n	13:35-14:00 Genome assembly from metagenomic reads (Jenn
 i Hultman)\n	14:00-14:30 Feedback and wrap up\n \n\nLanguage:  EnglishPr
 ice:          Free of charge\n\nhttps://events.prace-ri.eu/event/
 602/
SUMMARY:Metagenomics Data Analysis Workshop @ CSC
URL;VALUE=URI:https://events.prace-ri.eu/event/602/
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