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PFS0165

Basics of metagenome analysis

The subject areas covered include:

- Experimental design

- Introduction to DNA extraction and library construction for metagenomic projects

- Bioinformatic analysis of metagenomic data: data standards and submission, processing of raw data, assembly, functional annotation, overview of databases, retrieval and analysis tools.

- Pros and cons of metagenomics methods

The course contains five intense days of seminars, lectures and mandatory tutorials. Prior to the course students are expected to apply for an account at UPPMAX and complete computer exercises regarding working in unix/linux environment. Also, after the course the students will get an assignment that needs to be completed in order to get the course credits.

Kursplan

PFS0165 Basics of metagenome analysis, 3,0 Hp

Ämnen

Biologi

Utbildningens nivå

Forskarnivå

Förkunskapskrav

Admitted to a postgraduate program in animal science, biology, food science, or related subjects. Basic knowledge of R and working on a command line.

Mål

After completing the course the students are expected to

- Know the basic workflow of metagenomics research;

- Know the basic principles and concepts needed to understand the backgrounds of metagenomics research and to design a study;

- Submit data to public resources for metagenomics;

- Analyze metagenomics data using freely accessible tools available online;

- Interpret results and compare with other metagenomics datasets;

- Discuss the pitfalls and challenges in the different steps of the sample collection, processing and data analysis



Innehåll

The subject areas covered include:

- Experimental design

- Introduction to DNA extraction and library construction for metagenomic projects

- Bioinformatic analysis of metagenomic data: data standards and submission, processing of raw data, assembly, functional annotation, overview of databases, retrieval and analysis tools.

- Pros and cons of metagenomics methods

The course contains five intense days of seminars, lectures and mandatory tutorials. Prior to the course students are expected to apply for an account at UPPMAX and complete computer exercises regarding working in unix/linux environment. Also, after the course the students will get an assignment that needs to be completed in order to get the course credits.

Examinationsformer och fordringar för godkänd kurs

Participation in the lectures and successful completion of mandatory tutorials and assignments.

Ytterligare information

Teachers will include researchers from SLU, staff from the SLU Bioinformatics Infrastructure (SLUBI) and invited guests. The course is organized by the SLU research school Organism Biology. There is no tuition fee. Participants are expected to bring their own laptop for the practical computer exercises and to arrange and familiarize themselves with software and UPPMAX user accounts according to instructions from the organizer prior to the course start.