Next Generation Sequencing - data handling and analyses (2 ECTS)
Find your way around
This is the unofficial web page for the PhD course "Next Generation Sequencing - data handling and analyses (2 ECTS)" arranged by University of Gothenburg (Life Sciences) and ForBio - the Research School in Biosystematics. Here is where updated information about the course will be posted. The official course web page can be found here.
Next Generation Sequencing is an umbrella term for various high throughput sequencing methods (e.g. 454 pyrosequencing and Illumina sequencing). These methods are efficient ways of generating large amounts of data, and advances in this field is rapidly changing the way biological science is conducted. The amount of data that is now available to biologists introduce new ways of addressing questions on species relationship or population genetic processes, but also presents challenges in data handling and analysing. This course will present different sequencing methods and introduce the steps necessary to prepare, store and handle data. Special emphasis will be put on hands-on exercises in handling the large datasets that are generated in a NGS project.
- Those of you who need help accessing the wireless network during the course will receive help on Monday before the exercises begin.
Welcome everyone! (MT)
Lessons to be learned from genome sequencing (KJ)
Presentation of the Gothenburg Bioinformatics Network (HHE)
Genome sequencing of Atlantic cod (KJ)
Principles and problems of de novo genome assembly (LN)
Exercise: De novo assembly hands-on (LN) Handout and slides
Overview of a NGS project (MAR)
BILS and Cluster resources in Sweden (MAR)
Working in a cluster environment - An interactive lecture, part I (MT) Handout
Managing and querying large volumes of data: the MySQL database - Lecture and Exercise (HN) Handout
Next generation sequencing to study polyploid evolution (AKB)
Next generation sequencing to study polyploid evolution (AKB) Slides
Working in a cluster environment - An interactive lecture, part II (MT) Handout
Visualization of NGS data - Introduction and comparison of software packages (YB) Handout and Slides
Choosing models for phylogenetic analysis (GJ) Lecture notes and Slides
Working with Large Files: The Importance of a Good Text Editor (JN) Slides
Working with Large Files: Why Editing Large Files is A Bad Idea (JN) Slides
Exercise: Working with Large Files: From Many (Sequences) to One (Tree) (JN)
- Professor Kjetill Jakobsen, Centre for Ecological and Evolutionary Synthesis (CEES), Univ. of Oslo. (KJ)
- Dr. Lex Nederbragt, CEES, Univ. of Oslo. (LN)
- Dr. Anne Krag Brysting, CEES, Univ. of Oslo. (AKB)
- Dr. Magnus Alm Rosenblad, Department of Cell- and Molecular Biology, Univ. of Gothenburg. (MAR)
- Dr. Johan Nylander, Natural History Museum, Univ. of Oslo. (JN)
- Dr. Graham Jones, Department of Plant and Environmental Sciences (DPES), Univ. of Gothenburg. (GJ)
- Dr. Henrik Nilsson, DPES, Univ. Gothenburg. (HN)
- Dr. Marcela Davila Lopez, Department of Medical Biochemistry and Cell Biology, Univ. Gothenburg. (MDL)
- Dr. Yann Bertrand, DPES, Univ. of Gothenburg. (YB)
- Hannah Hansen Erlandsson, Genomics Core Facility, Univ. of Gothenburg. (HHE)
- Dr. Mats Töpel, DPES, Univ. of Gothenburg. (MT)
For the Monday lecture:
- Star et al. (2011) The genome sequence of Atlantic cod reveals a unique immune system. Nature 477, pp. 207–210. (pdf)
The supplemental information to this paper is of particular intrest to course participants, as it describes much of the bioinformatics used in the cod genome project.
For the Monday exercise (in preferred order):
- Pop (2009) Genome assembly reborn: recent computational challenges. Briefings in Bioinformatics. vol 10. no 4. 354-366. PDF
- Miller et. al (2010) Assembly Algorithms for Next-Generation Sequencing Data. Genomics 95(6): 315–327. PDF
- Narzisi et. al (2011) Comparing De Novo Genome Assembly: The Long and Short of It. PLos One. Vol 6. Issue 4. PDF
- Bao et. al (2011) Evaluation of next-generation sequencing software in mapping and assembly. Journal of Human Genetics 56, 406–414. PDF
- Earl et. al (2011) Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research. PDF
For the Tuesday lecture on computer clusters, as well as all exercises during the week:
- An Introduction to the Linux Command Shell For Beginners
Despite its misleading title (Bash is GNU not Linux!), this document provides a short introduction to most of the Bash commands and features you need for the course.
- Steve's Bourne / Bash Scripting Tutorial
A very nice and short shell scripting tutorial. After reading this one, you'll be able to solve many repetitive tasks easily.
- Bash Guide for Beginners
A little to advanced for this course, but a good reference manual to have around. I suggest you start by checking out the glossary section on page 146.
For the lecture on phylogenetics on Friday:
- Joseph Felsenstein (2004) Inferring Phylogenies. Sinauer Associates. ISBN: 0878931775.
Those of you who arrive in Gothenburg by train or buss can catch a tram (nr. 2 heading for Högstorp, 6 - Kortedala or 13 - Högstorp) to Linnéplatsen, which is the tramstop closest to Slottskogens Hostel and Änggårdens B&B, where rooms have been booked for ForBio members (breakfast is included). From there it is only a short walk to Conference Centre Wallenberg where the lectures and exercises will take place. The name of the lecture hall is Lyktan, and it should be easy to find once you arrive at the conference center. If you want to go directly from the central station to where the lectures will be, you can take tram nr. 7 (heading for Tynnered) or buss 58 or 753 to tramstop Medecinaregatan. The easiest way of buying Buss or tram tickets is to send an SMS with the message GV to +46 31 724 50.
Visa NGS course på en större karta