Preparation of genomics libraries for an emerging next-gen sequencing platform – Course and Conference Office

EMBL Course

Preparation of genomics libraries for an emerging next-gen sequencing platform


Course overview

This course will focus on the latest state-of-the-art sequencing platform technology and novel library preparation protocols. We will start with experimental design, focusing on the hands-on library preparation (including best practices, standards, and potential pitfalls), concluding with sequencing of libraries, bioinformatic evaluation & best practice. For this purpose we will use, for the first time ever in the settings of the practical course, the cutting-edge sequencing platform AVITI (https://www.elementbiosciences.com/products/aviti), which was developed by Element Biosciences and is currently entering the next-gen sequencing (NGS) field. An evaluation of the technology in conjunction with the newly developed library preparation reagents by New England Biolabs (NEB) will be important for the scientific community and course participants to assist their decision if to adopt the new sequencing technology. The course will cover a complete workflow, such as library preparation and sequencing. The course participants will also learn about its tips and tricks and will also use bioinformatics tools required for data processing, quality control and initial data analysis.

Beside the practical exercises, lectures and discussion sessions, the course will offer the opportunity to learn more about transferring the knowledge gained during the course to the home institute of the participants as well as the implementation of this new technology into the environment of genomics core facilities. During the course participants will prepare two types of NGS libraries, gDNA-Seq and mRNA-Seq. We offer the opportunity to provide a maximum of 2 samples. Those samples must be shipped to Heidelberg prior to the course and must meet quality criteria of EMBL GeneCore. Generated libraries will be used for shallow sequencing.


This course is directed towards wet-lab molecular biologists, scientists and technicians who want to assess and use the AVITI technology. A focus will be on applicants from member states and their genomics core facilities. This audience can best disseminate the knowledge gained during the course and serve scientists at their home institutes.


  • Presentation of the latest state-of-the-art sequencing technology (Element Biosciences, the AVITI system)
  • Hands-on training on genomic library preparation with upcoming state-of-the-art reagents
  • Setting up an AVITI sequencing run
  • Basics in data handling and analysis

Learning outcomes

The NGS field is entering a new phase of sequencing platforms available to the community and for their various applications. One crucial eplatform is the Aviti sytem by Element Bioscinces. During the course, its participants will:

  • be exposed to the cutting-edge sequencing technology
  • learn to apply novel NEBNext NGS library preparation reagents and protocols
  • learn about the benefits and bottlenecks of different systems
  • be provided with guidance on the implementation of sequencing technologies into the core facility environment

What past participants say about this course

“I truly recommend this course to anyone interested in RNASeq. We were pushed to go below the limits of RNA input to construct libraries and it was an exciting challenge. The spirit of science “go beyond our limits” was present through all of the course. The knowledge sharing environment with all the participants, trainers, and speakers, made this one of the best courses I have ever attended.” – Anna Sofia Varanda, University of Aveiro, Portugal


Speakers, trainers, and staff

Chris Mason

Weill Cornell Medicine


(Virtual Speaker)

Michael Petridis

New England Biolabs Inc.


Scientific organisers

John Baeten

Element Biosciences

The Netherlands

Course organisers

Preliminary programme

Got something to say? Tweet it! #EMBLSeqLibPrep 

  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 1 – Monday 6 November 2023
Time (Europe/Berlin)SessionLocation
13:00Arrival at EMBL
13:15 – 13:45Welcome of participants / registrationFlex lab A&B
13:45 – 14:15EMBL intro and House notes (incl. safety)Flex lab A&B
14:15 – 14:30Course overviewFlex lab A&B
14:30 – 16:00Icebreaking activity (Introduction round and “Challenges and Expectations”, each participant 2 slides)Flex lab A&B
16:00 – 16:30Coffee break
16:30 – 18:00Lab: Get familiar with equipment and bead processingTBC
18.00 – 19:00DinnerEMBL canteen
19:00Departure to HotelATC entrance
Day 2 – Tuesday 7 November 2023
Time (Europe/Berlin)SessionLocation
09:00 – 09:10Overview of the dayFlex lab A&B
09:10-10:00Lecture: Get familiar with the library prep protocolFlex lab A&B
10:00-12:30Lab I: sample preparation, End Prep dA-Tailing, Ligation, PCR setTBC
12:30-13:30Lunch BreakEMBL cantenn
13:30-14:30Lab II: Clean Up and Sample QuantificationTBC
14:30-15:00Coffee Break
15:00-16:00Lecture: Introduction of the AVITI sequencing platformFlex lab A&B
16:00-18:00Preparation and initiation of sequencing runTBC
18:00-19:00Tips & Tricks with concurrent Pizza DinnerTBC
Departure to Hotel
ATC entrance
Day 3 – Wednesday 8 November 2023
Time (Europe/Berlin)SessionLocation
09:00 – 09:10Overview of the dayFlex lab A&B
09:10 – 10:00Lecture: TBDFlex lab A&B
10:00 – 11:00Data processing, quality control ITBC
11:00 – 11:30Coffee break
11:30 – 12:30Bioinformatics ITBC
12:30 – 13:30LunchEMBL Canteen
13:30 – 15:30Bioinformatics IITBC
15:30 – 16:00Coffee Break
16:00 – 17:00Lecture title
Chris Mason – Weill Cornell Medicine, USA (virtual speaker)
Flex lab A&B
17:00Bus Heidelberg downtown and sightseeingATC entrance
19:30Dinner & Networking at local restaurant (NEB sponsored)TBC
Day 4 – Thursday 9 November 2023
Time (Europe/Berlin)SessionLocation
09:00 – 09:10Overview of the dayFlex lab A&B
09:10 – 10:00Lecture: TBDFlex lab A&B
10:00 – 11:00Lecture: Consideration on implementation of sequencing into the Core facility environment Vladimir Benes – EMBL Heidelberg, GermanyFlex lab A&B
11:00 – 11:30Coffee break
11:30 – 12:30Tour through GeneCore Facility and closer look at the AVITI systemTBC
12:30 – 13:30Lunch BreakEMBL Canteen
13:30 – 15:00Final Discussion roundFlex lab A&B
15:00 – 15:30Coffee Break
15:30 – 16:30Lecture: TBDFlex lab A&B
16:30 – 17:15Feedback round and closing remarksFlex lab A&B
17:15Bus to Heidelberg train station and city centerATC entrance

Practical information

Registration fees and motivation letter

The course is limited to 16 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks. Participants are expected to book and pay their own accommodation and travel expenses. 

Academia575 €
PhD Student575 €
Industry1100 €

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed. We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

Confirmation and payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation letter submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.


  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For detailed instructions, please watch our video on how to submit a course motivation letter.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial assistance

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.

Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

– up to €400 for participants travelling to an EMBL Course within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant (EMBO Practical Courses only)

For EMBO Practical Course participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of €500 can be awarded per participant applying for an EMBO childcare grant. 

Boehringer Ingelheim Fonds travel grant

Applies to selected courses only. Availability will be indicated during the motivation letter submission process.

This grant covers costs related to your attendance at the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.

Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course

– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course


You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

For the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.


The scientific organisers will select the recipients of all financial assistance during the motivation letter selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the course. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.


Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.

Accommodation and shuttles


Single rooms have been reserved for 5 nights (5-10 November 2023) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code NEB23-01). We recommend that all course participants stay at the ISG Hotel which is the dedicated hotel for the course.

Local transport

Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For further information on getting to EMBL Heidelberg visit our Travel Information page.

For enquiries about accommodation and local transportation please refer to the FAQ page.

Technical requirements and event software

Technical requirements

Below you will find the software and technical requirements for this course.

  • Participants need to bring their own laptops, which will be used to remotely access EMBL virtual machines with pre-installed software.
  • You will need admin rights to install the software required to access the virtual machines. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.
  • If you have a non-standard HDMI port (other than type A), you need to bring an adaptor.
  • Keyboard and PC mouse are available for use with a standard USB port. If you have a different port type, such as USB-C, you will need to bring your own.

Event software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Additional information

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

COVID-19 related questions

COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.


Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other events, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.


EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

Media kit

Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.

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Date: 6 - 9 Nov 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Application: 14 Aug 2023


  • John Baeten
    Element Biosciences, The Netherlands

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