Training school on bioinformatics for amplicon and shotgun metagenome analysis 14.-18.9.2015

Date & Place:

September 14th – 18th, Technische Universität Braunschweig, Hans-Sommer-Straße 65, Room HS65.4 in the Gauss-IT-Zentrum, Braunschweig, Germany

Organizers: Jacqueline Rapmund (Jacqueline.Rapmund@helmholtz-hzi.de), Andreas Bremges (Andreas.Bremges@helmholtz-hzi.de), Philipp Münch (Philipp.Muench@helmholtz-hzi.de)

Lecturers: Dr. Martin Hartmann (martin.hartmann@microbiome.ch), Dr. Alice McHardy (Alice.McHardy@helmholtz-hzi.de), Dr. Alex Sczyrba (asczyrba@techfak.uni-bielefeld.de), Dr. Christopher Quince, Dr. Folker Meyer.

Overview: The aim of this five day workshop will be to give students an overview of the tools and bioinformatics techniques available for the analysis of next generation sequence data from microbial communities. The format will comprise a mixture of lectures and hands-on tutorials where students will process example data sets in real-time. Students will also be encouraged to bring their own data for analysis. You can find the latest updates to the workshop agenda here: http://www.bioinformatics-platform.dzif.de/?page_id=50

The workshop comprises two parts:

Part I will focus on the analysis of amplicon sequences, for example 16S rRNA or fungal ITS, generated using next generation sequencing platforms: principally Illumina, but we will also touch other platforms. The entire process from initial sequence data through paired-end read assembly, quality filtering, OTU clustering, and taxonomic classification will be addressed during the first day. Instructions on data processing using state-of-the-art bioinformatic tools (e.g. USEARCH, QIIME, MOTHUR) will be provided. The second day will put emphasis on community analysis and ecological interpretation including, diversity estimations, multivariate statistics, indicator species analysis, and probabilistic models. A detailed tutorial on community analysis using R will be provided.

Part II will focus on the analysis of shotgun metagenome sequence data from microbial communities. This will cover lectures and tools for de novo sequence assembly, similarity- and composition-based tools for the taxonomic assignment (binning) of unassembled and assembled samples, draft genome recovery for abundant community members, gene prediction and an overview of functional annotation methods, as well as the “one stop shop” MG-RAST system for computational metagenome analysis. For shotgun sample analysis, please email BIFO-Trainingschool@helmholtz-hzi.de in advance with details for your sample.

Workshop application

Send the following information to BIFO-Trainingschool@helmholtz-hzi.de

  • Email header: Registration for computational metagenomics training school
  • First and last name
  • Affiliation
  • Days of attendance of training school
  • Dates for hotel reservation
  • DZIF membership: Yes/No
  • One paragraph describing the student’s motivation for attending the course and specification of the level of experience working on the command line with linux/unix systems: 1(0-49h), 2 (50-500h) or 3 (>500h). The latter is to allow the correct pitching of content – basic Linux and sequence analysis skills will be helpful.  Applications received before Monday June 29th will be considered and students selected who will benefit most from the training and by order of their applications. Students from any career level from under-graduate to professorial can attend but this is a hands-on workshop and preference will be given to people who will analyse their own data at some point in the future. Workshops are open to all, but DZIF members will be given preference.

 The Deadline for the registration is 29 June 2015.

Accomodation

Best Western Hotel Braunschweig http://goo.gl/rOn7JA

Dresdenstr. 10 D- 38124 Braunschweig Fon: +49 (0)531 / 26421-0 Fax: +49 (0)531 / 26421-200

E-Mail: braunschweig@plazahotels.de

www.bestwestern.de / www.plazahotels.de/deutsch/default.htm

Special negotiated rate: 89 Euro per night, including breakfast and free wireless internet access

Travel Information

Arrival from Hannover Airport

S-Bahn line S5 from Hannover airport – Hannover central station approximately every 30 min. Duration of travel approximately 17 min. Alternatively, a taxi will take approximately 25 min.

Arrival from Hannover central Station

Train from Hannover central Station – Braunschweig central station approximately every 30 min. Duration of travel approximately 45 min.

Arrival from Braunschweig central Station to course venue (Gauss-IT-Zentrum Braunschweig, Hans-Sommer-Straße 65)

Tram M19 approximately every 15 min. Duration of travel approximately 18 min.

Arrival from Best Western Hotel

Bus 431 approximately every 10 min. from  Dresdenstraße to Braunschweig central station (stand A), duration of travel approximately 9 min.

Wait about 8 min in Braunschweig central station ( stand A) and take tram M19 to Pockelsstraße, duration of travel approximately 10 min.

Hotel information

Best Western Hotel Braunschweig Dresdenstraße 10, 38124 Braunschweig

You will find the Best Western Hotel Braunschweig located in the quiet residential area of Braunschweig. The city center is easily reached in five minutes. Free parking is available directly outside the hotel. All of the 129 guest rooms are newly renovated, spacious and equipped with 42-inch flat screen satellite television and free Wi-Fi. You can relax in the complimentary sauna after an eventful day. In the morning our large buffet breakfast is waiting for you. Three conference rooms for up to 30 guests are available on the ground floor.

Logo News

6. Januar 2016

Workshop on Pipeline Programming and Linux Basics

From 02.-04.02.2016 the workshop „DZIF Pipeline Programming and Linux Basics“ will be run in Braunschweig. For more information […]

2. September 2015

Microbial Genome Annotation & Comparative Genomics Workshop

From 16.-17.11.2015 a workshop on „Microbial Genome Annotation & Comparative Genomics“ takes place in Gießen. […]

CLC bio Workshop

From 03.-04.11.2015 a CLC Workshop takes place in Gießen. For more information please click here.

de.NBI Late Summer School 2015 in Microbial Bioinformatics

From 20.-26.09.2015 the de.NBI Late Summer School 2015 in Microbial Bioinformatics takes place in Gießen. […]

25. März 2015

Workshop on Pipeline Programming and Linux Basics

From 26.-28.05.2015 a workshop „DZIF Pipeline Programming and Linux Basics“ will be run in Braunschweig. For more information please click […]