Metagenomic data analysis

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This course will run subject to demand. Please register your interest here for future training courses. We will inform you of new events and new locations as they become available.

Date:

winter 2018/19 (2 days)£599/£449)

Potential Locations:

CEH Lancaster, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP Location map & travel directions
CEH Wallingford, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB Location map & travel directions
CEH Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB Location map & travel directions
CEH Bangor, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd, LL57 2UW Location map & travel directions

Cost:

£ 599 regular

£449 registered students

Refreshments are included in the price. Accommodation is not included in the price.

Short Course Description:

This 2-day course will teach you how to perform metagenomics analysis with the software packages Qiime2 and R.

Day 1: Understanding the basics of work on the command line, followed by strategies to analyse different types of microbial data (amplicon and shotgun)

Day 2: In the morning, you will prepare sample datasets and analyse them in Qiime2 utilizing its different plug-ins. In the afternoon, you will analyse the same dataset in R with the Dada2 pipeline, followed by multivariate statistical analysis in R. You will then compare the results of the different pipelines.

Learning outcomes:

By the end of the course, participants will understand how to use Qiime 2 and R to prepare raw amplicon and shotgun metagenomic data for analysis, and run some of the statistical tools available in both software packages.

Accommodation:

Accommodation is not included in the cost. Some venues have low-cost university accommodation on site or nearby. More detail: see FAQ

Places:

15

Level:

Beginner

undergraduate-level knowledge of microbial ecology and fieldwork design.

Course Leader:

Dr Katja Lehmann, Microbial Ecologist and Bioinformatician,

Centre for Ecology & Hydrology. Dr Lehmann has been a member of the NERC Bioinformatics Analysis Facility Wallingford and has taught bioinformatics to early careers researchers

Target Audience:

MSc and PhD students and early career researchers working on microbial sequencing datasets

 

This course will run subject to demand. Please register your interest here for future training courses. We will inform you of new events and new locations as they become available.

 

Course delivery:

Blended learning, with lectures, discussions and independent learning times with elements of problem-based learning

Relevant links and key publications:

Lehmann, K. "Sampling of riverine or marine bacterial communities in remote locations: from field to publication." Marine Genomics: Methods and Protocols (2016): 1-11.