• Event
  • Scientific training

Metagenomics: from bench to data analysis 2016

To provide an overview of the main aspects involved in metagenomics from the bench to data analysis and discussion around the interpretation and actual examples of the impact and applications of metagenomics derived research.

Start date:

19 September 2016

End date:

23 September 2016

Time:

12h00 - 13h00

Venue:

Earlham Institute

Registration deadline:

15 July 2016

Cost:

£300.00

About the event.

What is the workshop about?

A substantial part of the course will be devoted to bioinformatics resources and tools relevant in metagenomics data analysis. Participants will start at the bench and end in front of the computers for a problem solving activity utilizing the bioinformatics training they will be receiving during the course.

What will it cover?

To provide an overview of the main aspects involved in metagenomics from the bench to data analysis and discussion around the interpretation and actual examples of the impact and applications of metagenomics derived research.

What will I learn?

  • An overview of NGS for metagenomics and metatranscriptomics including current projects
  • Knowledge of 16S Experimental Design including primer design and sources of error
  • Hands on experience in: DNA isolation, QC of the DNA, NGS library construction and loading the sequencing platform
  • An overview of software for analysis and interpretation of metagenomics datasets and some basic analytical workflows
  • Hands-on experience of a case study dataset including FastQC, trimming and host removal
  • Understanding assembly principles and the latest metagenomics assembly tools
  • Hands on experience in metagenomics assembly
  • Using MEGAN to explore metagenomic and metatranscriptomic data including taxonomic and functional annotation, multiple comparison methods and production of publication quality images
  • An overview and hands on experience in public data resources for metagenomics e.g. IMG/M, EBI Metagenomics, MG-RAST

Target Audience:

This course is aimed at advanced PhD students and post-doctoral researchers who are doing or planning to start research in the field of metagenomics.

Scientific Organisers:

  • Emily Angiolini, Earlham Institute (EI), UK
  • Kirsten McLay, Earlham Institute (EI), UK
  • Leah Catchpole, Earlham Institute (EI), UK
  • Richard Leggett, Earlham Institute (EI), UK
  • Mark Alston, Earlham Institute (EI), UK

Programme.

Day 1 - 19 September 2016

Time

Topic

12:00 - 13:00

Registration and Lunch

13:00 - 13:15

Welcome and introduction to the Earlham Institute

13:15 - 14:45

Short talks by participants

14:45 - 15:00

Coffee break

15:00 - 16:00

Lecture: what is metagenomics?

16:00 - 17:00

Lecture: introduction to Next Generation Sequencing of metagenomic samples

Day 2 - 20 September 2016

Time

Topic

08:30 - 09:00

Morning coffee

09:00 - 11:00

Practical session in the wet lab: extraction of metagenomic DNA and quality control

11:00 - 11:30

Practical Session in the wet lab: NGS library construction - DNA fragmentation and end repair

11:30 - 12:00

Coffee break (incubation time)

12:00 - 12:30

Practical session in the wet lab: clean up procedure

12:30 - 13:00

Practical session in the wet lab: NGS library construction - A'Tailing

13:00 - 14:00

Lunch break

14:00 - 14:30

Practical session in the wet lab: NGS library construction - clean up procedure

14:30 - 15:45

Practical session in the wet lab: NGS library construction - Adapter ligation and clean up

15:45 - 16:15

Coffee break

16:15 - 16:30

Practical Session in the wet lab: NGS library construction - PCR set up

16:30 - 17:00

Lecture: 16S experimental design

17:00 - 17:30

Lecture: How quantitative are 16S surveys?

Day 3 - 21 September 2016

Time

Topic

08:30 - 09:00

Morning coffee

09:00 - 10:30

Practical session: review of QC results and loading the sequencing platform

10:30 - 11:00

Coffee break

11:00 - 11:45

Tour of the Earlham Institute

11:45 - 12:00

Q&A

12:00 - 13:00

Lunch

13:00 - 14:00

Setting up VMs and recap to Linux

14:00 - 15:00

Lecture: introduction to tools and approaches for analysing and interpreting metagenomic datasets

15:00 - 15:30

Coffee break

15:30 - 17:00

Lecture and hands on session: Next Generation Sequencing data analysis for metagenomics

Day 4 - 22 September 2016

Time

Topic

08:30 - 09:00

Morning coffee

09:00 - 09:30

Introduction to "MEGAN"

09:30 - 11:00

Hands on session "MEGAN" - generating a MEGAN file

11:00 - 11:30

Coffee break

11:30 - 12:30

Lecture and hands on session: assembly of metagenomic samples

12:30 - 13:30

Lunch

13:30 - 15:00

Lecture: metatranscriptomics

15:00 - 15:30

Coffee break

15:30 - 17:00

Hands on session: analysis and visualisation with EBI metagenomics

Day 5 - 23 September 2016

Time

Topic

08:30 - 09:00

Morning coffee

09:00 - 10:30

Case studies

10:30 - 11:00

Coffee break

11:00 - 11:45

Case studies

11:45 - 12:00

Feedback and wrap up

12:00 - 13:00

Lunch and departure

Fees and accommodation.

Registration fee

£300.00 which is inclusive of lunch and refreshments, course dinner and course materials. Accommodation and transport from/to hotel to EI will be an optional extra during registration if you are selected for the course.

Bursaries

There are €500 bursaries available for DEANN members upon application and successful selection to be used to cover registration and to put towards travel and/or accommodation as appropriate. Please contact Emily Angiolini for further details.