General NGS data analysis

  • Location : Dolný Smokovec, Slovakia
  • Date : August 14 - 21, 2016
  • Attendees : 30 participants, 13 speakers

General NGS data analysis

Summer School in Bioinformatics & NGS Data Analysis (NGSchool2016) was held on August 14-21, 2016 in Dolný Smokovec, Slovakia. In the course of one week, the participants attended 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. The school was mainly addressed to students and researchers in early stage of their careers. Nevertheless, we also invited more advanced researchers to apply.


Materials from the school are available on GitHub. We covered the following topics:

  • introduction to Linux and Bioinformatics focusing on NGS-related analyses
  • general handling of NGS data
    • data formats (FastQ, SAM, BAM, VCF)
    • quality control
  • de novo genome & transcriptome assembly
  • 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
  • bisulphite sequencing, ChIP-Seq & Hi-C data analysis
  • GWAS & integration of molecular data
  • applications of NGS in biomedicine

We taught both, command-line (Linux) and online (Galaxy) tools. People having no prior experience with Bioinformatics were welcome, but strong motivation was desired! Participants were supposed to bring their own laptops with Ubuntu installed! We provided some toy examples, but we encouraged people to bring their own datasets. The course was held in English.


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

Welcome & Shot talks
Day 1:
Introduction to LinuxRoman Cheplyaka
Introduction to Bioinformatics & NGSTomáš Vinař / Broňa Brejová
Day 2:
Genome & transcriptome assemblyLeszek Pryszcz / German Demidov
Functional genome annotationMarina Marcet-Houben
Introduction to Statistics & RGerman Demidov
Day 3:
CNV detectionGerman Demidov
Differential expressionLeszek Pryszcz
Library construction for NGSPaulina Stachula
Day 4:
ChIP-seqMaciej Łapiński
From ChIP-seq to Hi-CBartek Wilczyński
Bisulphite sequencingRussell Hamilton
Shot talks #2Leszek Pryszcz
Day 5:
Molecular data integrationJacek Marzec
Day 6:
NGS & BiomedicineSophia Derdak
Day 7:
Recap & farewell