4th RoBioinfo Seminar: NGS technologies

Bucharest

25-27 February. 2019

09:00

Next-Generation Sequencing Data Analysis

When?
Where?
Registration
Schedule
Organisers
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Conclusions
Beer and science event

When?

25-27 February 2019

Where?

University of Bucharest, Romania

Registration

Please fill in the form until 25th of January: https://goo.gl/forms/eiVClvRCwM1KP4Ni1

Applicants will be asked to write a motivational letter, in which they explain 1. why the course is important for their career development 2. why they should be the ones selected to participate in the training, and not others.
In the past, we have received three times more applications than the number of available spots in the trainings. To avoid disappointment, please make sure that you do your best to convince us that you are the best person to participate in the training.

A registration fee of 50 euros is required from academia participants to cover meals and dinner. Bursaries are available (up to 10 places; with 50% reduction or full fee exemption), and are awarded on merit and motivation. Mention in the registration form if you intend to apply for it.

Registration will open in January 2019.

Requirements

A fundamental understanding of Molecular Biology and basic knowledge of Statistics, Unix command line, R and/or Python are assumed. Suggested resources:

Unix: http://www.ee.surrey.ac.uk/Teaching/Unix/
Perl: https://learn.perl.org/books/beginning-perl/
Python: https://thepythonguru.com/

Speakers

The list of confirmed speakers and trainers is:

Viorica Chelban (University College London, Institute of Neurology, UK)
Hugues Richard (Pierre and Marie Curie University, Paris, France)
Petr Daněček (University of Cambridge, Cambridge, UK)
Valeriu Ohan (Wellcome Sanger Institute, Cambridge, UK)
Aleksandra Świercz (University of Technology, Poznan, Poland)
Bogdan Mirăuță (European Bioinformatics Institute, Cambridge, UK)

Schedule

Day 1: DNA sequencing

Time	Subject	Trainer/Speaker
9:00 – 9:15	Welcome note	TBD
9:15 – 10:30	Hands-on: Introduction to Unix environment	Valeriu Ohan
10:30 – 11:00	Coffee Break
11:00 – 11:30	Theory: File formats, QC	Petr Daněček
11:30 – 12:00	Hands-on: FASTA, FASTQ files	Valeriu Ohan
12:00 – 13:00	Lunch
13:00 – 14:00	Theory: Alignment	Petr Daněček
14:00 – 14:30	Hands-on: SAM, BAM files	Valeriu Ohan
14:30 – 15:00	Coffee Break
15:00 – 16:00	Theory: Variant calling	Petr Daněček
16:00 – 16:30	Hands-on: VCF, BCF files	Valeriu Ohan
16:30 – 17:30	Hands-on: An NGS pipeline exercise	Valeriu Ohan, Petr Daněček
18:30	Beer and Science	The event will take place at The Pub, in Universitatii Square. See Beer and science event for details.

Day 2: RNA sequencing

Time	Subject	Trainer/Speaker
9:00 – 10:00	Talk: NGS in rare genetic disease discovery	Viorica Chelban
10:00 – 10:30	Theory: An introduction to RNA-Seq	Hugues Richard
10:30 – 11:00	Coffee Break
11:00 – 12:00	Hands-on: RNA-seq (I)	Hugues Richard
12:00 – 13:00	Lunch
13:00 – 14:00	Hands-on: RNA-seq (II)	Hugues Richard
14:00 – 14:30	Theory: Analysis of RNA –Seq data for a research paper. Essential steps from read counts to results.	Bogdan Mirăuță
14:30 – 15:00	Coffee break
15:00 – 17:00	Hands-on: Analysis of RNA –Seq data for a research paper. Essential steps from read counts to results.	Bogdan Mirăuță
19:00	Dinner

Day 3: Genome assemblies

Time	Subject	Trainer/Speaker
9:00 – 10:30	Theory: Genome Assembly	Aleksandra Świercz
10:30 – 11:00	Coffee Break
11:00 – 12:00	Hands-on: Genome Assembly	Aleksandra Świercz
12:00 – 13:00	Lunch
13:00 – 13:30	Talk: TBD	Diana Bolca
13:30 – 14:30	Talk: Sequencing with long read technologies (Oxford Nanopore and Pacific Biosciences)	Aleksandra Świercz
14:30 – 15:00	Coffee break
15:00 – 15:15	Talk: TBD.	TBC
15:15 – 15:30	Talk: TBD.	TBC
15:30 – 16:00	Talk: New kids on the block: 10x Genomics, Dovetail Genomics, Optical maps.	Petr Daněček
16:00-16:30	Farewell

Organisers

Marieta Costache (University of Bucharest, Romania)
Sorina Dinescu (University of Bucharest, Romania)
Robi Tăcutu (Institutul de Biochimie al Academiei Române, Bucharest, Romania)
Valeriu Ohan (Cambridge, UK)
Alexandru Salceanu (Bucharest, Romania)
Monica Abrudan (Cambridge, UK)

Beer and science event

“Beer and science” is an informal event, where scientists present a science topic in 5 minutes, in a pub, to their peers, but also to non-scientists. Our goal is to promote interdisciplinary talks between speacialists in Biology, Medicine, Computer Science and Engineering.

We encourage simple and easy to digest presentations.

At the end of each presentation, we encourage participants to join in the discussions and ask questions. This is a good opportunity for scientists to discuss their faced issues with the broader community. Discussions between the speaker and public can generate ideas for solving existing problems. Also, it can lead to new research ideas.

The event will take place at The Pub, in Universitatii Square.