ForBio and UiO/IBV course: Bioinformatics for environmental DNA sequencing
For mapping and exploring communities of both micro- and macroorganisms, high throughput sequencing of environmental DNA has become a powerful approach. One can either analyze the total DNA content to obtain knowledge about which genes are present (DNA metagenomics) or sequence a selected PCR amplified marker (DNA metabarcoding) to obtain information about the taxonomic composition. We will focus on the latter approach in this course. The students will be introduced to important analytical bioinformatics approaches from processing of raw sequence data to establishment of the OTU/sample matrix and retrieval of taxonomic identity of the sequences.
Important themes will be (1) filtering and quality assessment of high throughput sequence data, (2) error correction and/or clustering of high throughput sequence data, and (3) taxonomic annotation of high throughput sequence data. We will also touch upon some further downstream analyses, including network analyses and evolutionary placement of short-read sequences onto backbone phylogenies. Applications of a wide suite of tools will be presented, including VSEARCH and DADA2.
The course overlaps with ForBio/Tromsø Museum, UiT course "DNA Metabarcoding: Data processing and interpretation". Both courses will provide conceptual insights into the workflow going from raw data to a data matrix but will introduce the students to different approaches. While overlapping thematically, they will introduce algorithmically different solutions, implemented as different software tools: Obitools (Tromsø course) and DADA2, VSEARCH and swarm (at the UiO course). The latter suite of tools is often used in studies of microbial/fungal communities.
Ramiro Logares, Anders Krabberød, Micah Dunthorn, Torbjørn Rognes and Håvard Kauserud.
This course is registered at the University of Oslo as BIO9905MERG1 and amounts 5 ECTS (if the course report is submitted) and 3 ECTS (without a submission of course report). Course attendance certificates will be issued by ForBio for those participants who are not registered at the UiO.
PhD candidates from the University of Oslo should apply for classes and register for examinations through Studentweb.
Financial aid: Participation of the Norwegian-affiliated students/postdoctoral researchers will be covered by ForBio. Other applicants will need to secure own funding to cover travel to Oslo, accommodation and subsistence for the course duration. There is no course fees. Please register for ForBio membership here.
Registration and selection process: Please fill in the online application here. ForBio reserves the right to give priority to PhD students whose research focuses on DNA metabarcoding applications.
Recommended previous knowledge
Basic knowledge in molecular biology and DNA analyses. Basic knowledge in R and some insight in programming/scripting will be highly advantageous.
This is an intensive online course over five days (May 3-7).
A project report will be compulsory and must be submitted two weeks after the course.
The report will be marked as passed/not passed.
Grades are awarded on a pass/fail scale. Read more about the grading system.
Explanations and appeals
For more information about the application/admission to the course contact Galina Gusarova firstname.lastname@example.org and for the questions regarding the course content: Håvard Kauserud email@example.com and Galina Gusarova firstname.lastname@example.org.
Registration deadline is February 28, 2021.