MG-RAST workshop (17-18 Sept 2014)

MG-RAST (the Metagenomics RAST; http://metagenomics.anl.gov) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples.

This 2-day workshop will offer researchers opportunities to analyze shotgun metagenomics high-throughput sequencing datasets with MG-RAST, understand the user interface, provide metadata and perform analysis. Special attention will be paid to the API and the R interface, together with general tips and trick for data processing. Sample data will be provided for hands-on analysis.

This workshop will acquaint researchers with MG-RAST sequence analysis tools, enable them to implement their research with MG-RAST, provide hands-on training with real sequence data and offer opportunities to discuss analysis strategies directly with the MG-RAST developers.

Instructors

Folker Meyer (Argonne National Laboratory and University of Chicago)
Andreas Wilke (Argonne National Laboratory and University of Chicago)

Schedule

day1: Wednesday September 17, 2014, 9:00-17:30

1. MG-RAST overview and user interface
• browse and search public data
• understanding the pipeline and its limitations
• understanding the overview page (a first glance at your data)
• check primer/probe coverage in Probe Match
2. Analysis and comparison with the web interface
• review concepts (abundance profile)
• adjusting parameters
• comparison of multiple samples
• exporting data

day2: Thursday September 18, 2014, 9:00-17:30

1. R Interface (matR) and the API
1. using R
2. the MG-RAST API
3. simple script examples using the API
4. exporting from MG-RAST to other software
2. Metadata GSC --- Standards and Data Submission
1. GSC genome standards
2. Entering metadata with MetaZen
3. Specialist topics
1. sequence pathology --- common problems with NGS and how to find them
2. to assemble or not to assemble?
3. details on the pipeline
4. scripting with MG-RAST

Venue

The course will be organised in the multimedia room of the Information and Communication Technology Department (DICT) at Ghent University, as this facilty has laptop computers for participants that cannot bring their own. Participants that work on their own laptop computer are invited to install a recent version of Firefox. This venue will be made freely available by DICT, with coffee and soda drinks free of charge for all participants.

Organizing committee

Prof. Dr. Peter Dawyndt (Ghent University)
Prof. Dr. Anne Willems (Ghent University)
ir. Bart Mesuere (Ghent University)
ir. Caroline De Tender (Institute for Agricultural and Fisheries Research; ILVO)

Contact

Prof. Dr. Peter Dawyndt
Department of Applied Mathematics, Computer Science and Statistics
Ghent University
phone: +32 9 264 4779
email: Peter.Dawyndt@UGent.be

Please fill up this form to register your participation to this workshop.

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Prof. Dr. Peter Dawyndt
 
Ghent University
Department of Applied Mathematics, Computer Science and Statistics (WE02)
Krijgslaan 281 (S9)
B-9000 Ghent
Belgium
 
Tel: (32)9.264.47.79
Fax: (32)9.264.49.95
Email: Peter.Dawyndt@UGent.be
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