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Phylogenetic Analysis Using R
October 14-18, 2019 (Spain)
Genetics and Genomics
Course Overview
Metagenomics is the study of the collection of genomes in an environment. Environments as diverse as Antarctic lakes, hot springs, or the human gut can be biologically characterized by extracting and sequencing DNA from samples taken from them. A characteristic of many of these samples is their complexity, posing difficulties to their analysis and characterization. However, metagenomics allows the taxonomic and functional characterization of samples. These two kinds of characterizations also enable the comparison of different habitats for biodiversity assessment.
In this course students will be introduced to the command line environment used to analyze high-throughput sequencing data (HTS). The initial cleaning steps that must be performed on every HTS dataset will be described and we will use the processed data for proper functional and taxonomical characterization of a metagenomic dataset. We will use methods such as mapping to whole genome databases, de novo assembly, gene annotation, building of non-redundant gene catalogue, and metagenomic species concept identification. Due to the wide usage of metabarcoding for the taxonomic characterization of an environment, we will also discuss amplicon sequencing strategies and data analysis. The course will be based on both theory and hands-on exercises.
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LOCATION
Alexander Hotel
Gerakári, Municipality of Amari, 74 061
Rethymno
Crete, Greece
DATES
April 1st-5th, 2019
LANGUAGE
English
COURSE LENGTH & ECTS
40 hours on-site.
This course is equivalent to 2 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.
The recognition of ECTS by other institutions depends on each university or school.
PLACES
Places are limited to 20 participants and will be occupied by strict registration order.
Participants who have completed the course will receive a certificate at the end of it.
Requirements
Graduate or postgraduate degree in Life Sciences and basic knowledge of Statistics and Genetics. Prior experience with bioinformatics is not required but some experience with running commands in R or Linux will be a plus.
All participants must bring their own personal laptop (Windows, Macintosh, Linux). Participants with PC’s operating Windows on them will be asked to install VirtualBox with Ubuntu (free of cost). Instructions will be sent prior to the beginning of the course.
Program
Monday, April 1st, 2019.
- Terminal:
- Introduction to shell / R.
- Raw data manipulation:
- Quality control.
- Cleaning.
Tuesday, April 2nd, 2019.
- Reference-based analysis:
- Mapping.
- Reference-free analyses I:
- De novo assembly.
- Reference-free analyses II:
- Ab initio gene prediction.
- Annotation.
- Metagenomic species concept.
Wednesday, April 3rd, 2019.
- Filtering:
- Threshold decision making.
- Core identification.
- Taxonomic and functional profiling I:
- General characterization.
- Taxonomic and functional profiling II:
- Metabolic pathways.
Thursday, April 4th, 2019.
- Statistical analyses:
- Abundance.
- PCA.
- Significance tests.
- Metabarcoding:
- DAMe.
- QIIME.
Friday, April 5th, 2019.
- Putting results into context:
- Design challenges and biological context.
- Group presentations.
- Questions.
Fees
- Course Fee
- Early bird (until December 31st, 2019):
- 540 € *
- Regular (after December 31st, 2019):
- 675 € *
- This includes course material, coffee breaks and lunches (VAT included).
* Participants from companies/industry will have an extra charge of 100 €.
- Course Fee + Accommodation Package
- Early bird (until December 31st, 2019):
- 540 € * + 350 € = 890 €
- Regular (after December 31st, 2019):
- 675 € * + 350 € = 1025 €
- This includes course material, coffee breaks, transportation from and to Heraklion city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
* Participants from companies/industry will have an extra charge of 100 €.
20 % discount will be applied to your fee If you belong to any of the Institutions listed HERE. Discounts (see Funding below) are not cumulative and apply only on the fee.
We offer the possibility of paying in two instalments (contact the course coordinator).
Accommodation
If you choose the Accommodation Package you will be hosted at Alexander Hotel in Gerakári village (take a look at the venue), in shared en-suite twin rooms, although you will only share rooms with other course participants. There is a possibility that the rooms will be mixed. If this is an inconvenience for you, and you would prefer to stay in an all-female or all-male room, please indicate so in the “Comments” field of the Registration form (below).
If you prefer to stay in a single en-suite room, you can do so with a supplementary charge.
The Accommodation Package includes transportation from the centre of Heraklion to the venue and back, at the start and end of the course, respectively. The trip takes around 1 hour 50 minutes each way.
If you do not wish to take the Accommodation Package, you can find a few other options in the surrounding area. However, please be aware that access to and travelling around the area requires a private vehicle as public transport is scarce. Therefore, course participants will find choosing the Accommodation Package more convenient.
Alexander Hotel, Gerakári
Alexander Hotel twin room
Alexander Hotel, Gerakári
Alexander Hotel, Gerakári
Schedule
Course Schedule
- Monday to Friday:
- 9:30 to 13:30 Lessons.
- 13:30 to 15:00 Lunch (included).
- 15:00 to 19:00 Lessons.
Accommodation Package Schedule
- Sunday:
- 19:00 Meeting at the Archaeological Museum of Heraklion to take the bus to Gerakári.
- 20:45 Registration in Alexander Hotel.
- 21:15 Dinner.
- Monday to Thursday:
- 8:30 to 9:00 Breakfast.
- 20:30 Dinner.
- Friday:
- 8:30 to 9:00 Breakfast.
- 18:15 Meeting point in Alexander Hotel to take the bus to Heraklion.
- 20:00 Arrival at the Archaeological Museum of Heraklion.
The schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.
Funding
Discounts
Former participants will have a 5 % discount on the Course Fee.
Furthermore, a 20 % discount on the Course Fee is offered for members of some organizations (Organizations with discount). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).
Unemployed scientists living in Greece, as well as PhD students based in Greece without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.
Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.
Organizer
Collaborators
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Transmitting Science started in 2012 to manage specialized courses and workshops we were already organizing within our own Partnerships. Up to date, we have already run more than 120 advanced courses in different topics related to Life Sciences.
All the courses are self-financed with participant’s fees and we strive to keep the fees to the minimum necessary for running them.
Our courses cover a wide range of research methods and are aimed at postgraduate students, postdoctoral researchers and established academics from all over the world.
All the courses are self-financed with participant’s fees and we strive to keep the fees to the minimum necessary for running them.
Our courses cover a wide range of research methods and are aimed at postgraduate students, postdoctoral researchers and established academics from all over the world.