News: Physalia-courses: 16S rRNA gene Metabarcoding Workshop
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gravatar for carlopecoraro2
3.1 years ago by
carlopecoraro21.2k
Berlin
carlopecoraro21.2k wrote:

16S rRNA gene metabarcoding workshop

Monday 3rd to Friday 7th April 2017 in Berlin, Germany http://www.physalia-courses.org/courses/course8/

Instructor: Dr. Alexandre Barretto de Menezes (http://www.physalia-courses.org/instructors/t5/)

Overview: The 16s rRNA gene has become the standard marker for prokaryote phylogenetic analysis, and combined with high-throughput sequencing technologies it is widely used to infer the structure and composition of microbial communities. Due to the continuous improvements in sequencing technologies and bioinformatics tools, there is a wide choice of methods for sequencing and analysing 16S rRNA gene assemblies. This workshop is designed to give students the necessary background and practical experience of the strategies for the analysis of the diversity and structure of prokaryote communities, covering i) experimental design and primer choices; ii) wet-lab and library preparation options; iii) sequence quality control and analysis and iv) statistical analysis of microbial community data. The many sequencing and analysis options will be discussed, whereas a more in-depth tutorial using real sequence data will provide an opportunity for the student to practice 16S rRNA sequence analysis from raw sequence files to ecological interpretation. Course material, such as presentation slides and necessary model data, will be provided to the students.

Targeted audience and assumed background: This workshop is intended for students and researchers interested in microbial ecology but who are not yet very familiar with the techniques involved. Choosing the appropriate primers, library preparation kits, sequencing methodologies and bioinformatics pipelines can be quite daunting to the uninitiated. This workshop will allow researchers interested more confidence in their methodology and analyses choices. The target audience include students of animal or plant microbiomes as well as those studying environmental microbial communities. It is assumed that the workshop attendees are interested in performing 16S rRNA metabarcoding using the Illumina MiSeq platform, although other sequencing technologies will be discussed during the workshop. Knowledge of Linux and R or familiarity with working in the command line will be helpful, but for those new to the area detailed instructions will allow students to follow the workshop. Students will need to have a computer running either on Linux or a Linux virtual machine running on MacOX/Windows computers. Contact the instructor at ademez@gmail.com if in doubt about computational requirements.

Where: Seminar room at Molecular Parasitology, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 14, 10115 Berlin

Workshop structure: The workshop will consist of both lectures and practical classes. Background information will be provided to help workshop attendees choose the appropriate experimental design, primers, sequencing library preparation kits and to contextualise the bioinformatics and statistical analysis methods. Practical tutorials will be conducted on a step-by-step basis to guide the student from when receiving data from a sequence provider to obtaining plots and tables describing microbial community diversity, structure and relationships to environmental variables or host data.

Session contents: Session 1: the 16S rRNA gene Session 2: sequencing experimental design and initial hands-on exercises Session 3: library preparation for MiSeq sequencing Session 4: practical session on sequence analysis pipelines Session 5: mothur tutorial Session 6: alternative tutorial combining USEARCH and mothur Session 7: QIIME and Ninja OPS Session 8: using statistical tools provided in mothur and QIIME Session 9: other analysis tools in R and Linux Optional session 10: wrap up and questions

Further information: The cost is 430 euros (VAT included) including refreshments and course materials. We also offer an all-inclusive package at 695 euros (VAT included), including breakfast, lunch, dinner, refreshments, accommodation, course and transfer from/to the main city’s airports.

ADD COMMENTlink modified 13 months ago • written 3.1 years ago by carlopecoraro21.2k
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gravatar for carlopecoraro2
2.8 years ago by
carlopecoraro21.2k
Berlin
carlopecoraro21.2k wrote:

Dear all,

here's an updated version of the syllabus for the "16S rRNA gene Metabarcoding" workshop, 3-7 April 2017 in Berlin (Germany), in which we have added in the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2).

Please you can find more information about the course on our website: https://www.physalia-courses.org/courses/course8/

Instructor: Dr. Alexandre de Menezes (National University of Ireland Galway) https://www.physalia-courses.org/instructors/t5/

Further information:

There two packages available: 1) “only-course”, which costs 430 euros (VAT included) and includes refreshments and course material; 2) “all-inclusive” which costs 695 euros (VAT included) and includes refreshments, course material, accommodation and meals (breakfast, lunch, dinner).

Registration deadline: March 3rd, 2017

ADD COMMENTlink written 2.8 years ago by carlopecoraro21.2k
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gravatar for contact
13 months ago by
contact40
contact40 wrote:

Why Do We Perform 16S rRNA Sequencing?

16S rRNA as molecular marker 16S rRNA gene is characterized by ubiquity and evolutionary properties, which allow it to become an important molecular marker in microbial ecology. Carl Woese and George E. Fox pioneered the use of 16S rRNA in phylogenetics. And according to Yang et al. (Figure 2), red regions (V2 and V8) have a poor phylogenetic resolution at the phylum level. Green regions (V4, V5, and V6) are associated with the shortest geodesic distance, which implies that they may be the optimal choice for phylogeny-related analyses, including phylogenetic analysis of novel bacteria phyla.... https://www.cd-genomics.com/blog/index.php/why-perform-16s-rrna-sequencing/

ADD COMMENTlink written 13 months ago by contact40
0
gravatar for carlopecoraro2
13 months ago by
carlopecoraro21.2k
Berlin
carlopecoraro21.2k wrote:

We will run a new updated version of this Workshop next year in April: https://www.physalia-courses.org/courses-workshops/course30/

ADD COMMENTlink written 13 months ago by carlopecoraro21.2k
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