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Microbial community analysis of 16S data with Chipster
Date: 21.04.2020 9:00 - 21.04.2020 17:00
Location details: The event is organised at the CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. The best way to reach us is by public transportation; more detailed travel tips are available.
Language: english-language
lecturers: Eija Korpelainen
Jesse Harrison
  • 60 for-finnish-academics
  • 280 for-others
The fee covers all materials, lunches as well as morning and afternoon coffees.
The seats are filled in the registration order. If a cancellation is received five (5) business days prior to the course, the course fee will be refunded with the exception of a handling fee of 10 €. For no-shows and cancellations after the cut of date no refunds will be made. Registration can be transferred to someone else from the same organization without additional charge.

Payment can be made with electronic invoicing, credit card, or direct bank transfer. Note that for electronic invoicing you need the operator and e-invoicing address (OVT code) of your organization. Please also note that invoice reference is needed for electronic invoicing in your organization, so please have this available when registering.
Additional Information

This hands-on 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. Please note that this course focuses on microbiome analysis of amplicon sequencing data (as opposed to metagenomics where all the genes are sequences). The free and user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required.

Learning objectives

After this course you will be able to

  • preprocess amplicon sequencing data for microbial community analysis
  • compare the structure of microbial communities using ordinations and multivariate statistics and perform indicator species analysis

Course content

  • checking the quality of reads with FastQC
  • combining paired reads to contigs
    • screening sequences for length and ambiguous bases
    • removing identical sequences
  • aligning sequences to the Silva reference alignment
    • screening aligned sequences for alignment position, homopolymers
    • filtering alignment for empty columns and overhangs
    • removing new identical sequences
  • preclustering very similar sequences
  • removing chimeric sequences
  • classifying sequences to taxonomic units
    • removing unwanted lineages
  • counting species per sample
  • statistical analysis
    • comparing the structure of microbial communities using ordinations (RDA) and multivariate statistics (PERMANOVA, PERMDISP)
    • performing indicator species analysis

Target audience

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 analyse data themselves, but who need to understand the concepts in order to discuss with bioinformaticians.