#NGSchool2017: Single-cell sequencing

Summer School in Bioinformatics & NGS Data Analysis (#NGSchool2017) will be held on 10-17 September 2017 in CBiES, Jachranka 81 k/Warszawy. In the course of one week, the participants will attend the series of lectures and workshops, covering various aspects of Computational Biology, focusing on state-of-the-art techniques related to Next-Generation Sequencing (NGS) and its application in research, health-care and industry. It is mainly addressed to students and researchers in early stage of their careers. Nevertheless, we invite also more advanced researchers to apply. 

In 2017, we'll focus on data analysis from single-cell technologies. As before, the course will cover wide range of topics, selected by popularity among attendees. Example topics include:

  • introduction to Linux and Bioinformatics focusing on NGS-related analyses
    • programming in R / Bioconductor, Python
    • data visualisation
  • general handling of NGS data
    • data formats (FastQ, SAM, BAM, VCF)
    • Quality Control
  • de novo genome & transcriptome assembly
    • dealing with heterozygous/polymorphic genomes
    • gene prediction and functional annotation
  • detection of SNPs & SVs (deletions, duplications, inversions, translocations)
    • prediction of functional effects of detected variants
  • RNA-seq & differential expression analyses
  • Epigenomics: bisulphite sequencing, ChIP-seq, ChIA-PET, ATAC-seq, Hi-C data analysis
  • applications of NGS in biomedicine
    • GWAS & integration of molecular data
    • personalised medicine
    • microbial genomics
  • low input & single-cell: sample preparation & data analysis

You will learn both, command-line (Linux) and online tools. People having no prior experience with Bioinformatics are welcome, but strong motivation is desired! 
Participants should bring their own laptops with Ubuntu installed! We will provide some toy examples, but we encourage you to bring your own datasets. 
The course will be held in English.

 

Programme

You can find detailed programme draft below. We will have morning (9-13) and afternoon (14-18) sessions, with coffee breaks ~11:00 and ~16:00. Breakfast will be served from 8:00, lunch at 13:00 and dinner around 19:00. 

Workshops (in italic) last typically 4 hours and consists of theoretical introduction and practical exercises. In the evenings, we'll have lecture-only sessions (marked with underline), shot-talks, discussions and some more relaxed activities (optional). 

Day Time Activity Host
Day 0: Sunday      
  15:00 Introduction to Linux, Bioinformatics & NGS Broňa Brejová & Tomáš Vinař
  18:00 Welcome & Shot talks #1 Leszek Pryszcz
Day 1: Monday      
  9:00 Data visualisation Przemysław Biecek
  14:00 Molecular data integration Jacek Marzec
  20:00 Shot talks #2 Leszek Pryszcz
Day 2: Tuesday      
  9:00 Workflows & pipelines Alina Frolova
  14:00 Genome & transcriptome assembly from single-cell data Andrey Prjibelski
  20:00 Beta & Bit games Przemysław Biecek
Day 3: Wednesday      
  9:00 Detection of SNPs & structural variations (CNVs) Tomasz Gambin
  14:00 Introduction to Statistics / RNA structure probing German Demidov / Łukasz Kiełpiński
  18:00 Team-working: Moving forward and enjoying science together / Open science - discussion Panagiotis Theodorakis /
Paweł Szczęsny
  20:00 Chilling evening BBQ #1 & #OpenScience contest  
Day 4: Thursday      
  9:00 Functional genome annotation Marina Marcet-Houben
  14:00 Differential ChIP-seq

Aliaksei Holik

  20:00

RNase H sequence preferences influence antisense oligonucleotide efficiency and have shaped the HIV-1 genome

Łukasz Kiełpiński
Day 5: Friday      
  9:00 Single-cell RNA-seq analysis Davis McCarthy
  14:00 Differential expression analysis Davis McCarthy
  18:00 Genome structure & function [keynote] Noam Kaplan
Day 6: Saturday      
  9:00 Single-cell Hi-C data analysis Aleksandra Galitsyna
  14:00 ATAC-seq / Microbial genomics Katarzyna Kędzierska / Adam Witney
  18:00 Problem-oriented sessions Check FB group for details
  20:00 Chilling evening BBQ #2  
Day 7: Sunday      
  10:00 Recap & farewell Leszek Pryszcz

Speakers

Materials

You can find all #NGSchool2017 materials here

Social events

We'll organise set of social events, including BBQ nights, movie night, volleyball games and kayaking. We'll make sure, there is plenty of fun, beside hard working during workshops ;) 

Photos

You can find photos from all our events in the gallery and on Twitter (#NGSchool2017).

Registration

Registration will be opened between 1 May and 30 June 2017 (11:59 CET). To register, follow this link: http://bit.ly/ngschoool2017_registration

We will offer ~30 places. Successful applicants will be notified two weeks after registration deadline.

The expenses related to the course, including full boarding oscillate around €550. The registration will be free of charge given we get sufficient funding. We'll post more details in the end of May 2017. In addition, we are planning to accept limited number of participants that will be able to cover all the expenses by themselves. This year, we have received the grant from International Visegrad Fund, so the registration for #NGSchool2017 covering accommodation and full boarding will be free of charge