NSC course: High Through-put Sequencing: technology basics, applications and bioinformatic analysis (Oct. 25-27 2011)

NSC course: High Through-put Sequencing: technology basics, applications and bioinformatic analysis (Oct. 25-27 2011)

The Norwegian Sequencing Centre is offering a course in basic applications and bioinformatics analysis of High Throughput Sequencing data Oct 25-28 in Oslo.

The course has two independent components:

  • an introduction to High Throughput Sequencing (afternoon of Tuesday the 25th)
  • two days of application specific sessions (Wednesday the 26th and Thursday the 27th). Each application specific session will last for two days and applicants must thus pick which one they wish to follow:
    • variant calling (SNPs, indels and structural variation)
    • de novo genome assembly

You may apply for:

  • just the introduction
  • one of the application sessions
  • both the introduction and one of the application sessions

Note that the number of participants is limited by room and staff constraints. We will of course do our best to give everyone that applies a place on the course. However, if more people register than there are available places, then we will need to select participants from those that have registered. This will NOT be done on a purely first come - first served basis. Other factors taken into consideration when selecting participants will be:

  • whether participants are likely to benefit from the course
  • whether participants represent a diverse set of home institutions/groups, e.g. it may be necessary to limit the number of participants from any given group/lab
  • whether participants are NSC users or not

The course will take place at the University of Oslo, Blindern campus. There is no registration fee, but participants will have to arrange for their own accomodation. During Wednesday and Thursday, we will serve coffee, tea and refreshments. Lunch can be bought in the cantina of a neighbouring building.

Check out the progam below. There is no registration fee. REGISTRATION IS NOW CLOSED.

NOTE that the Friday following the course (October 29th), the NSC seminar will take place, with sessions on sessions 1) Human Genomics 2) Evolutionary Genomics and 3) Launch of the PacBio platform here at NSC. Check out the seminar program here.


Tuesday Oct 25th 13:00-17:00 Introduction to High Throughput Sequencing

Presenters: Tim Hughes (NSC), Robert Lyle (NSC), Ave Tooming klunderud (NSC), Lex Nederbragt (NSC), Gregor Gilfillan (NSC).

An overview of High-Throughput Sequencing (HTS) technologies

  • Basic technological principles (Sanger, illumina, 454, PacBio, etc)
  • Features of the different technologies (sample preps, read length, realistic yield, error rates, biases, costs, etc)
  • Applications of the different technologies: what can you sequence (DNA, mRNA, microRNA, etc) and which technology should you use.
  • Do I really need HTS? What is the right technology for my project?

Presentation of the Norwegian Sequencing Centre

Understanding basic output files

  • Including basic quality control of this output.

Resources for analysis of HTS data

 

Parallel sessions (choose one):

Principles vs. practice: presentations will alternate between explaining principles/concepts and demonstrating current practice. In addition, there will be practical session where attendees will get to use relevant software themselves.

Software for the practical session will be run on the Unix platform and some basic unix skills definitely an advantage. We will, however, set the course up in such a way that attendees without a Unix background will still get to participate in and learn from these hands-on sessions.


Wednesday - Thursday Oct 26th-27th 9:00-17:00 Variant calling (SNPs, indels and structural variation) using High Through-put sequencing data

Teachers

Tim Hughes (NSC), Ying Sheng (NSC), Robert Lyle (NSC), Yvan Strahm (Avdeling for Medisinsk Genetikk, Oslo University Hospital), Mariann Kulseth (Avdeling for Medisinsk Genetikk, Oslo University Hospital)

Target audience

This session should be relevant to anyone with an interest in identifying variants in a sample relative to a reference genome.

Laptop

Participants are recommended to bring a laptop to the course running unix or mac osx. We will also have some laptops available for those attendees that do not have access to such a machine. We will have wireless internet accounts available.

Overview of topics (each topic will have a principles and practical component)

  • Quality control of a fastq file
  • Read alignment
  • SAM/BAM format
  • Basic read classification
  • Assessing coverage of a capture experiment
  • Alignment refinement (duplicate removal, realignment, quality recalibration)
  • Variant calling
  • VCF format
  • Variant annotation
  • Assessing variant lists
  • Browsing a resequenced sample using IGV

There is no registration fee. REGISTRATION IS NOW CLOSED.


Wednesday - Thursday Oct 26th-27th 9:00-17:00 De novo genome assembly

Teachers

Lex Nederbragt (NSC, CEES - Dept. of Biology, Univ. of Oslo, http://flavors.me/flxlex), Nick Loman (School of Biosciences, University of Birmingham, United Kingdom, http://pathogenomics.bham.ac.uk/staff/nloman.html), Karin Lagesen (CEES), Ave Tooming klunderud (NSC and CEES), Trine Ballestad Rounge (CEES, Dept. of Biology, Univ. of Oslo)

Target audience

This session should be relevant to anyone with an interest in performing de novo assemblies for organisms for which no reference genome is available, or in order to compare the assembly to a reference genome.

Laptop

Participants are required to bring a laptop to the course running unix or mac osx. We will have wireless internet accounts available.

Overview of topics

  • principles and problems behind de novo genome assembly
  • basic-level understanding of the different algorithmic approaches to assembly (Overlap Layout Consensus, kmer/de Bruijn graph)
  • basics behind the choice of sequencing platform for de novo assembly
  • quality control and filtration of sequence reads before assembly
  • hands-on work with a few of the most popular assembly programs, e.g. newbler, MIRA, velvet, CLCBio
  • assembly metrics, assembly quality control
  • comparison of different assemblies with each other and with a reference genome
  • due to practical reasons, we will mainly use bacterial genome datasets, but may touch upon aspects relevant for larger genomes is there is an interest in this. Also, de novo transcriptome will  not be covered in this session

There is no registration fee. REGISTRATION IS NOW CLOSED.

Published Aug. 31, 2011 1:00 PM - Last modified Mar. 21, 2013 12:48 PM