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.)