• Advanced Courses in Life Sciences

    Header of Genetics and Genomics at Transmitting Science

Course – 2nd Edition

An introduction to Metagenomics and Metabarcoding

April 1st-5th, 2019, Barcelona (Spain)

Genetics and Genomics

Genetics and Genomics

Course An introduction to Metagenomics and Metabarcoding

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.

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.

Contact

courses@transmittingscience.com

REGISTRATION IS CLOSED

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LOCATION

DATE

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.

M. Lisandra Zepeda-Mendoza instructor for Transmitting Science

Dr. M. Lisandra Zepeda-Mendoza
Chr. Hansen – Bacterial Physiology & Improvement
Denmark

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 November 30th, 2019):
  • 534 € *

    (427.20 € for Ambassador Institutions)

  • Regular (after November 30th, 2019):
  • 667 € *

    (533.60 € for Ambassador Institutions)

  • 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 November 30th, 2019):
  • 804 € *

    (697.20 € for Ambassador Institutions)

  • Regular (after November 30th, 2019):
  • 937 € *

    (803.60 € for Ambassador Institutions)

  • This includes course material, coffee breaks, transportation from and to Barcelona city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

You can check the list of Ambassador Institutions. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com

Schedule

Course Schedule

Participants will make their own way

  • Monday to Friday:
    • 9:30 to 13:30 Lessons.
    • 13:30 to 14:30 Lunch (included).
    • 14:30 to 17:00 Lessons.

The class 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.

Course + Accommodation Package Schedule
  • Monday:
    • 19:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Els Hostalets de Pierola. If you are planning to arrive later, you can find more information on how to get there.
    • 20:00 Registration in the Hostel.
    • 20:30 Dinner.
  • Tuesday to Thursday:
    • 08:00 to 09:00 Breakfast
    • 9:30 to 13:30 Lessons
    • 13:30 to 14:30 Lunch (included)
    • 14:30 to 17:00 Lessons
    • 20:30 Dinner
  • Friday:
    • 8:00 to 9:00 Breakfast.
    • 9:30 to 13:30 Lessons
    • 13:30 to 14:30 Lunch (included)
    • 14:00 to 16:30 Lessons
    • 17:00 Meeting point in the Hostel to take the bus to Barcelona city.
    • 18:30 Arrival at Plaza Catalunya (Barcelona).

The class 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.

Accommodation

If you choose the Accommodation Package you will be hosted at Rural House Can Carol, in shared en-suite rooms, although you will only share rooms with other course participants (male or female only).

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 Barcelona city to the venue and back, at the start and end of the course, respectively. The trip takes around 1 hour each way. 

If the number of participants exceeds the available rooms at Can Carol, some of them could be accommodated in the Hotel Tall del Conill, by registration order. The hotel is at 10 minutes walking, although transport will be provided in the morning and after dinner. Lunches and dinners will be with the whole group.

Accommodation is included from Sunday (check-in) to Friday (check-out). Breakfast, lunch and dinner are also provided during the week, starting from the dinner of Sunday to lunch of Friday (included).

Other accommodation options

If you do not want the Accommodation Package, accommodation is available in places other than Can Carol: Where to stay near the Venue.

Funding

Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).

Former participants will have a 5 % discount on the Course Fee.

20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in the country were the course will be held, as well as PhD students based in that country 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.

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