- 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
Organiser:
Enquiries:
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
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 ofpublication 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
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.
