Metabarcoding is a rapidly evolving technique that identifies DNA from a set of often unknown organisms and reveals microbial communities in unprecedented taxonomical resolution by using universal PCR primers and high-throughput sequencing. It increasingly gains importance in almost all fields of biological and medical sciences. Its wide application range includes biodiversity assessment and monitoring, diet analysis, reconstruction of paleocommunities and more. The processing of metabarcoding data requires a broad range of skills at the interface of molecular biology, bioinformatics, biostatistics and biology/ecology.
In this workshop, the participants will be introduced to the workflow of microbiome research targeting the 16S- and 18S rRNA gene: preceded by an overview of the full process, this course is aimed at the analysis of high-throughput sequencing data with open-source and cross-platform software (mothur and R/Bioconductor packages) from the raw reads to the visualization of results. Theoretical content will be visualized and strengthened by practical exercises. Participants will practice during the workshop on prepared data sets.
- Linux terminal
- cutadapt
- mothur
- R and Bioconductor packages
- ShortRead
- gridExtra
- dada2
- DECIPHER
- phyloseq
- ggplot2
- reshape2
- vegan
- lme4
- car
- microbiome
- VennDiagram