This online course introduces the participants to microbiome analysis methods, tools, and file formats. It covers the whole workflow from quality control and filtering to quantification and statistical analysis using Mothur and Phyloseq tools integrated in the user-friendly Chipster platform. Please note that this course focuses on microbiome analysis of amplicon sequencing data (as opposed to metagenomics where all the genes are sequenced).The course consists of lectures and practical exercises. The lectures will be available as short videos, and the participants are requested to view them prior to the course. This gives you more time to reflect on the concepts so that you can use the course days more efficiently. The lectures are summarized and questions answered during the course.Learning outcomeAfter this course, you will be able topreprocess amplicon sequencing data for microbial community analysiscompare the structure of microbial communities using ordinations and multivariate statisticsPrerequisites and content levelThe free and user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required.The content level of the course is intermediate and the course is intended for life scientists who are planning to use 16S or other amplicon sequencing in their microbiome research. This course is suitable also for those researchers who do not plan to analyze data themselves, but who need to understand the concepts in order to discuss with bioinformaticians.AgendaDay 1, Thursday May 20 (10:00 - 15:30 EEST | UTC/GMT + 3 hours)Checking the quality of reads with MultiQCPreprocessing combining paired reads to contigsscreening sequences for length and ambiguous basesremoving identical sequencesAlignmentaligning sequences to the Silva reference alignmentscreening aligned sequences for alignment position and homopolymersfiltering alignment for empty columns and overhangsremoving new identical sequencesPreclustering, removing chimeric sequencesDay 2, Friday May 21 (10:00 - 15:30 EEST | UTC/GMT + 3 hours)Data tidying and analysisCreating and importing phyloseq input filesIncluding taxonomic assignments and OTU clusteringData inspection and tidying using phyloseqRemoving unwanted taxaFiltering singletons and doubletonsPrevalence filteringData transformation, ordination and conversionCLR, Hellinger and % relative abundancenMDS and db-RDADESeq2 format conversion and variance-stabilising transformationRelative abundance plotsCommunity comparisons using PERMANOVA, PERMDISP and DESeq2Lecturers:  Dr. Jesse Harrison (CSC), Dr. Eija Korpelainen (CSC)Language:  EnglishPrice:           Free of charge (2 training days)For further detailed information please visit:https://events.prace-ri.eu/e/MicrobialCommunityAnalysisChipster_2021 THE COURSE IS FULLY BOOKED and REGISTRATION IS CLOSED!If you have registered to the course and you are not able to attend, please CANCEL your registration in advanceby sending an email to patc@csc.fi.We have processed a limited waiting list. Please contact patc@csc.fi on that matter.We will keep those on the waiting list informed of whether participation will be possible.