Metagenomics Bioinformatics
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Date:
Monday 14 - Wednesday 16 September 2015Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Tuesday 14 April 2015Application deadline:
Friday 03 July 2015Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£395Registration closed
Overview
This course will cover the use of publicly available resources to manage, share, analyse and interpret metagenomics data, including both marker gene and whole gene shotgun (WGS) approaches. Delegates will gain hands-on experience using a range of data resources and tools, interspersed with lectures.
Analysing your own data: Please note that there may be an opportunity to analyse your own metagenomics data during the course, provided that it is submitted to the EBI Metagenomics Portal for analysis sufficiently in advance. If you do not have data to analyse, it may be worth identifying a project related to your work that is publicly available from the EBI Metagenomics Portal (//www.ebi.ac.uk/metagenomics/). Further details about how to submit data and deadlines for submission will be provided once your application has been successful.
Audience
This course is aimed at biologists who are beginning new projects in the field metagenomics research.
Prerequisites
Some practical sessions in the course require a basic understanding of the Unix command line and the R statistics package. Please ensure that you complete these free tutorials before you attend the course:
•Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
•Introduction and exercises for Bio-Linux 7, the Linux environment we will be using during the course: http://nebc.nerc.ac.uk/support/training/course-notes/past-notes/intro-bl7
•Basic R concept tutorials: www.r-tutor.com/r-introduction
Syllabus, tools and resources
During this course you will learn about:
- Data standards: Genomic Standards Consortium (GSC)
- Data generation: Next Generation Sequencing, amplicon-based approaches (ribosomal RNA)
- Data submission: ENA, SRA, Webin
- Data analysis: The EBI Metagenomics Portal, QIIME, HMMER, InterPro, GO, FASTQC
Outcomes
After this course you should be able to:
- Comprehend the minimum standards required for submission to comply with the Genomic Standards Consortium (GSC)
- Use a range of amplicon based (marker genes) and metagenomics tools including the EBI Metagenomics Portal
- Submit metagenomics data to public repositories
- Interpret results and compare them with other metagenomic datasets
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Monday 14th September | ||
| 09:30 | Registration | |
| 10:00 | An introduction to the EBI | Laura Emery |
| 10:30 | An introduction to NGS technologies | Laura Emery |
| 11:00 | Coffee/Tea break | |
| 11:30 | Introduction to metagenomics data analysis: workflows and public resources | Alex Mitchell/Hubert Denise |
| 12:30 | Lunch | |
| 13:30 | Data standards for metagenomics | Petra Ten Hoopen |
| 14:00 | Describing your data using standards and data submission to the European Nucleotide Archive (lecture/hands-on) | Petra Ten Hoopen |
| 15:30 | Coffee/Tea break | |
| 16:00 | Command line warm up (hands-on) | Alex Mitchell |
| 16:30 | Participants Presentation | Participants |
| 17:30 | Poster Session | |
| 19:00 | Dinner | |
| Day 2 - Tuesday 15th September | ||
| 09:00 | Quality control with hands on | Hubert Denise |
| 10:00 | Taxonomic analyses (lecture/hands-on) | Pier Luigi Buttigieg |
| 11:00 | Coffee/Tea break | |
| 11:30 | Taxonomic analyses cont. (lecture/hands-on) | Pier Luigi Buttigieg |
| 13:00 | Lunch | |
| 14:00 | Homology searching in metagenomic data sets | Rob Finn |
| 15:00 | Keynote lecture: Computational discovery of biosynthetic pathways in genomes and metagenomes | Marnix Medema |
| 16:00 | Coffee/Tea break | |
| 16:30 | Explore your own data (hands-on) | MG portal team |
| 18:00 | Close | |
| 19:30 | Dinner | |
| Day 3 - Wednesday 16th September | ||
| 09:00 | Functional and taxonomic analysis using the EBI Metagenomics Portal (lecture/hands-on) | Alex Mitchell |
| 10:00 | Coffee/Tea break | |
| 10:30 | Data analysis using R (hands-on) | Blaise Alako |
| 12:00 | Lunch | |
| 13:00 | Database building and searching using HMMER (hands-on) | Rob Finn |
| 14:00 | Explore your own data and Q & A (hands-on) | MG portal team |
| 15:30 | Course feedback and wrap up | Laura Emery |
| 16:00 | Departure | |