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Thu 13 Feb - Fri 14 Feb 2020
09:30 - 17:00

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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An introduction to long-read sequencing
BeginnersNew

Thu 13 Feb - Fri 14 Feb 2020

Description

Analysis of whole genome data unearths a multitude of variants of different classes, which need to be filtered, annotated and validated to arrive at a causative variant for a disease. The current short length sequences, whilst being excellent at identifying single nucleotide variants and short insertions/deletions, struggle to correctly map structural variants (SVs). Long-read sequencing technologies offer improvements in the characterisation of genetic variation and regions that are difficult to assess with short-read sequences.

The aim of this course is to familiarise participants with long read sequencing technologies, their applications and the bioinformatics tools used to assemble this kind of data. Lectures will introduce this technology and provide insight into methods for the analysis of genomic data, while the hands-on sessions will allow participants to run analysis pipelines, focusing on data generated by the Oxford Nanopore Technologies (ONT) platform.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • This is aimed for life scientists with little or no experience in long-read sequencing that are looking at implementing these approaches in their research.
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here
Prerequisites
  • The course is suitable for complete beginners and assumes no prior programming experience.
  • Basic knowledge of R and UNIX would be an advantage. An introduction to the the Unix system and shell is available here.
Sessions

Number of sessions: 2

# Date Time Venue Trainers
1 Thu 13 Feb   09:30 - 17:00 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Alba Sanchis-Juan,  Jonathan Stephens,  Nicholas Gleadall
2 Fri 14 Feb   09:30 - 17:00 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Alba Sanchis-Juan,  Nicholas Gleadall
Topics covered

Bioinformatics, Biology, Data handling

Objectives

After this course you should be able to:

  • Discuss advantages and limitations of the methods presented
  • Assess the quality of your sequencing run
  • Process reads and align them to a reference genome
  • Analyse and interpret long-read sequencing data for variant and stractural variant calling
Aims

During this course you will learn about:

  • Introduction to ONT devices
  • Wet lab preparation of libraries for Nanopore sequencing
  • Introduction to data processing of long-reads
  • Variant calling and quality control
  • Structural variant calling and quality control
  • Haplotype phasing
Format

Presentations, demonstrations and practicals

Timetable

Day 1 Topics
9:30 - 11:00 Introduction to ONT
11:00 - 11:15 Tea/Coffee Break
11:15 - 12:45 Sample preparation
12:45 - 13:30 Lunch (not provided)
13:30 - 15:00  Quality control
15:00 - 15:15 Tea/Coffee Break
15:15 - 16:45 Alignment
16:45 - 17:00 Wrap Up
Day 2
9:30 - 11:00 Variant calling pipeline
11:00 - 11:15  Tea/Coffee Break
11:15 - 12:45  Structural Variant pipeline
12:45 -13:30  Lunch (not provided)
13:30 - 15:00  Phasing
15:00 - 15:15 Tea/Coffee Break
15:15 - 16:45 Methylation pipeline
16:45 - 17:00 Wrap Up
Registration Fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Duration

2

Frequency

A number of times per year

Theme
Specialized Training

Booking / availability