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Manipulation of NGS Data for Genomic and Population Genetics Analyses
June 17-20, 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.
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 €.
We offer the possibility of paying in two instalments (contact the course coordinators). Discounts (see Funding below) are not cumulative and apply only on the fee, not to Accommodation Package or other options.
Accommodation
If you take the Accommodation Package option you will be hosted in Arolithos (take a look at the venue), in shared twin rooms with a shared bathroom, although you will only share rooms with other classmates. The possibility exists that rooms will be mixed. Therefore, if this is an inconvenience for you, and you require staying in a room with only women or only men, please indicate so in the “Comments” field of the Registration form (see below).
A supplemental charge will be added if you prefer to stay in a single room with private bathroom.
If you do not want the Accommodation Package, there are several accommodation options in Heraklion. However please be aware that it takes about 25 minutes by car from Heraklion to Arolithos and there is no public transport between both. Therefore course participants will find that staying in Arolithos is more convenient.
How to get to Arolithos from Heraklion, Chania or Rethimnon.
Arolithos street
Arolithos twin room
Arolithos twin room
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 point at Heraklion Archaeological Museum (Heraklion) to take the bus to Arolithos. If you are planning to arrive later, you can find more information on the Arolithos website.
- 19:30 Registration in the Youth Hostel.
- 20:00 Dinner.
- Monday to Thursday:
- 8:30 to 9:00 Breakfast.
- 20:30 Dinner.
- Friday:
- 8:30 to 9:00 Breakfast.
- 19:00 Meeting point in the Hotel to take the bus to The Archaeological Museum.
- 19:45 Arrival at 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
Former participants will have a 5 % discount on the Course Fee.
Unfortunately there are no scholarships available for this course. However 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).
Greek unemployed scientists, as well as Greek PhD students 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 coordinators. That would apply for a maximum of 1 place and it 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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Registration
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.