Introduction to Metagenomics (IN-PERSON)

PrerequisitesUpdated

This workshop will focus on the theory and applications of metagenomics for the analysis of complex microbiomes (microbial communities). We will cover a range of methods from the fastest, simplest and cheapest amplicon-based methods up to Hi-C metagenomics techniques that give highly detailed results on complex microbial communities. In addition to the theory, we will introduce several bioinformatic software packages suited for the analysis of metagenomic data, quality control and downstream analysis and interpretation of the results.

If you do not have a University of Cambridge Raven account please book or register your interest here.

• ♿ The training room is located on the first floor and there is currently no wheelchair or level access.
• Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
• Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
• Further details regarding eligibility criteria are available here.

• The course is aimed at biologists interested in microbiology, prokaryotic genomics, analysis of complex microbiomes and antimicrobial resistance.

Essential

• Basic understanding of high-throughput sequencing technologies.
  • Watch this iBiology video for an excellent overview.
• A working knowledge of the UNIX command line (course registration page).
  • If you are not able to attend this prerequisite course, please work through our Unix command line materials ahead of the course (up to section 7).
• A working knowledge of R (course registration page).
  • If you are not able to attend this prerequisite course, please work through our R materials ahead of the course.

Desirable

• A basic knowledge of phylogenetics inference methods (course registration page).
• A working knowledge of running analysis on High Performance Computing (HPC) clusters (course registration page).

Bioinformatics, Metagenomics, Data visualisation, Data handing, Data mining

During this course you will learn about:

• The main metagenomics approaches available for the study of microbial communities.
• When to apply different metagenomic approaches, their pros and cons and the time and resource requirements involved in each one.
• Bioinformatics workflows for the main approaches covered.

After this course you should be able to:

• Choose the best approach for your metagenomics project.
• Plan the time and resources needed for such a project.
• Select the required bioinformatics tools for analysing your data.
• Explain how commonly used metagenomics pipelines work and apply them to your data.
• Prepare for and deal with contamination issues.

Presentations, demonstrations

• Free for registered University of Cambridge students
• £ 60/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
• It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
• £ 60/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
• £ 120/day for all Industry participants. These charges must be paid at registration
• Further details regarding the charging policy are available here

3

Once a year

• Introduction to working with UNIX and bash (IN-PERSON)