Bioinformatics for environmental DNA sequencing
This course in collaboration with Digital Life Norway.
Dates: 3-7 May, 2021
Location: The course is arranged online
Lecturers: Håvard Kauserud (UiO), Ramiro Logares (Barcelona), Anders Krabberød (UiO), Micah Dunthorn (UiO)
Credits: 3 ECTS
Contact: Håvard Kauserud, University of Oslo, firstname.lastname@example.org
Background. For mapping and exploring communities of both micro- and macroorganisms, high throughput sequencing of environmental DNA has become a powerful approach. One approach is to sequence and analyze the total DNA content in a sample to obtain knowledge about which genes are present (DNA metagenomics). Another inference is to sequence a selected PCR amplified marker to obtain information about which organisms are present; the taxonomic composition (DNA metabarcoding). In this online course we will focus on the latter approach.
What will we teach? The students will be introduced to important bioinformatics approaches during DNA metabarcoding, ranging from processing of raw sequence data to establishment of the final OTU/sample matrix and retrieval of taxonomic identity of the sequences. Important themes will be (1) different sequencing techniques, (2) filtering and quality assessment of high throughput sequence data, (3) error correction and/or clustering of high throughput sequence data, and (4) taxonomic annotation of high throughput sequence data. We will also touch upon some further downstream analyses, including multivariate community analyses, network analyses and evolutionary placement of short-read sequences onto backbone phylogenies. Applications of a wide suite of tools will be presented, including DADA2 and VSEARCH. There will also be a few guest lectures, focusing on specific topics such as long-read metabarcoding and decontamination of metabarcoding data. In addition, some case studies will be presented. Further instructions and a selection of articles will be provided to course participants 2-3 weeks before course start.
What will you learn? You will learn about conceptual topics related to bioinformatics analyses of DNA-metabarcoding data and will be introduced to best practices. You will get experience in data processing using DADA2 and will be introduced to numerous other programs.
Prior knowledge requisites? Some programs, like DADA2, will be run in the R environment. Hence, some basic knowledge in R will be very helpful. Knowledge in (UNIX) command-line will also be advantageous. Otherwise, general knowledge about DNA sequencing and organismal biodiversity will make it easier to follow.
How will we teach? The entire course will run in zoom. The current covid situation will limit hands-on assistance, but we will conduct shorter sessions where you work with real data. We will also organize smaller discussion groups throughout the course.