Community analysis of amplicon sequencing data (16S rRNA)

This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. The course takes one day. You will learn how to

  • check the quality of reads with FastQC and PRINSEQ
  • remove bad quality data with Trimmomatic, PRINSEQ and Mothur
  • taxonomic classification with Mothur
  • statistical analysis for marker gene studies based on R packages vegan, rich, biodiversityR, pegas and labdsv

Course material (2017) is available at the course website and it includes

  • slides
    1. Introduction to community analysis by Anu Mikkonen
    2. Community analysis with Chipster
    3. Statistical analysis of marker gene data by Jarno Tuimala
  • lecture videos
  • exercises (the data is available on Chipster server in the example session listed in the exercise sheet, and we also provide ready-made analysis sessions which you can use as a reference when doing exercises on your own.)

Additional information

Resource type: course materials, Video

Authors: Eija Korpelainen, Maria Lehtivaara, Jarno Tuimala, Anu Mikkonen

External resources: