Bioinformatics for metagenomics and environmental sequencing
Dates: March 27-31 2017
Location: University of Oslo
Organiser: Håvard Kauserud
Registration: Now closed
Course code: BIO9905MERG1
Credits: 5 ECTS.
Evaluation: Report based, pass/fail
Program: downloaded from here
Suggested reading: here
High throughput sequencing (HTS) of PCR amplified markers (DNA metabarcoding or amplicon sequencing) is typically used to profile the taxonomic composition of environmental samples, qualitatively and partly quantitatively. The main aim with this course is to introduce participants to bioinformatics tools used for analyzing HTS-based DNA metabarcoding data. Important themes will be (1) filtering and quality assessment of HTS data, (2) clustering of HTS data, (3) taxonomic annotation, (4) diversity analyses, and (5) analyses of microbial community composition. The course will be a blend of presentations and hands-on computer sessions. Important programs that will be presented and used include SWARM, VSEARCH, QIIME, and mother. Statistical analyses will be run in R. We will provide relevant literature and links to software some weeks before the course start. Participants that want to run analyses on their own machine during the course must have them installed before the course (we do not provide support in this other than providing links to the programs). To obtain course credits a report must be handed in after the course.
The five-day intensive course will be run at the Department of Biosciences, University of Oslo during week 13 (27-31 March). Teachers will include Ramiro Logares, Marie Davey, and Torbjørn Rognes. The course is organized by Håvard Kauserud.