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Wed 6 May - Thu 7 May 2020
09:30, ...

Venue: Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

Provided by: Bioinformatics


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Introduction to metagenomics (ONLINE LIVE TRAINING)

Wed 6 May - Thu 7 May 2020


PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team be teaching the course live online, with tutors available to help you work through the course material on a personal copy of the course environment. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

This two days course will focus on the theory and applications of metagenomics, for the analysis of complex microbiomes (microbial communities). The course will include theoretical (~40%) and practical (~60%) training. We will start with the fastest, simplest and cheapest amplicon based methods and will go up to the Hi-C metagenomics methods that give highly detailed results on the complex microbial communities. The practical component will cover bioinformatics analysis of metagenomics.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.

Target audience
  • The course is aimed at biologists interested in microbiology, prokaryotic genomics, analysis of complex microbiomes and antimicrobial resistance.
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here
  • Knowledge of Linux/Unix command line is required.
  • We recommend attending the Introduction to working with UNIX and bash course. An introduction to the the Unix system and shell is also available here.
  • Basic knowledge on next-generation sequencing, microbiology is beneficial but not essential.

Number of sessions: 2

# Date Time Venue Trainers
1 Wed 6 May   09:30 - 17:00 09:30 - 17:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter) Dr Lajos Kalmar,  Marcus de Goffau
2 Thu 7 May   09:30 - 16:30 09:30 - 16:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter) Dr Lajos Kalmar,  Marcus de Goffau
Topics covered

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


After this course you should be able to:

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

During this course you will learn about:

  • The main metagenomics approaches
  • Their application and comparison on time and resource requirement
  • Bioinformatics pipelines for each main approach

Presentations, demonstrations


This is subject to change in line with the online training schedule.

Day 1 Topics
9:30 - 10:15 Presentation: Introduction to metagenomics
10:15 - 11:00 Lecture: Amplicon based metagenomics
11:00 - 13:00 Practical: Amplicon based metagenomics
13:00 - 14:00 Lunch (not provided)
14:00 - 15:00 Lecture: Extract metagenomic information from shotgun sequencing data without assembly
15:00 - 17:00 Practical: Shotgun metagenomics without assembly
Day 2
9:30 - 10:15 Lecture: Shotgun metagenomics with assembly
10:15 - 12:00 Practical: Shotgun metagenomics with assembly
12:00 - 13:00 Lunch (not provided)
13:00 - 14:00 Lecture: Hi-C metagenomics
14:00 - 16:00 Practical: Hi-C metagenomics
16:00 - 16:30 Q&A and wrap up
Registration fees
  • Free for registered University of Cambridge students
  • £ 50/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.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here



Once a year

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