Course Overview
Sequencing has become an essential tool in genetic and genomic analysis. It is increasingly important for experimental scientists to gain the bioinformatics skills required to analyse the large volumes of data produced by sequencers. This course aims to equip participants with the essential informatics skills required to begin analysing data and apply some of the most commonly used tools and resources for sequence data analysis. The programme covers prominent sequencing technologies, algorithmic theory, and principles of bioinformatics, with a strong focus on practical computational sessions using sequence analysis techniques and tools applicable to any species or genome size. A variety of applications will be covered from post-sequencing analysis, quality control, reference  alignment, and variant calling
Intended Audience
Applicants should be postdoctoral scientists, senior PhD students, junior faculty members or clinicians/healthcare professionals actively engaged in or soon to commence research involving sequencing data analysis
Keywords: Genome analysis, Sequencing, Unix, variant calling
Skill level of training: Beginner
Language: English
Credential awarded: No credential awarded
Type of training: Blended/hybrid learning
Venue of workshop: Distributed Classrooms
Dates for the workshop: 15 August - 10 October 2023
Workshop organisers: Wellcome Connecting Science and H3ABioNet
Participation: The course is available to any classroom who meets the requirements and to any participant who is able to attend a physical/online classroom, provided they have been selected via the selection process. Should a classroom decide to host a face-to-face classroom, the participant must be able to attend this classroom in person for the duration of the course.
Workshop Sponsors: Wellcome Connecting Science and H3ABioNet
 

Classroom applications

Registration for classrooms opens: Mon, 24/04/2023
Registration for classrooms closes: Fri, 19/05/2023
Link to classroom application form: <a href="https://redcap.h3abionet.org/redcap/surveys/?s=M38K9H33A9R4HTD8"; rel="nofollow noopener noreferrer" target="_blank">https://redcap.h3abionet.org/redcap/surveys/?s=M38K9H33A9R4HTD8</a>;
Notification date for successful classrooms: Thu, 01/06/2023
Maximum number of participants that may be accepted per classroom will be capped at 40

Participant applications

Registration for participants opens: Thu, 15/06/2023
Registration for participants closes: Thu, 29/06/2023
Participant registration link: <a href="https://redcap.h3abionet.org/redcap/surveys/?s=8RETJXACPA8CDL8M"; rel="nofollow noopener noreferrer" target="_blank">https://redcap.h3abionet.org/redcap/surveys/?s=8RETJXACPA8CDL8M</a>;
Syllabus and Tools

 The course will cover the following topics:

  • Intro to Unix/Linux & running workflows
  • Introduction to Sequencing Technologies
  • Sequencing data pre-processing and QC
  • Alignment to reference sequences
  • Variant calling and annotation

 

Prerequisites

The practical sessions will be taught exclusively through Unix/Linux. Therefore, participants are required to have some previous experience using the Linux operating system. This will be essential for participants to fully benefit from the course. There are numerous online introductory tutorials to the UNIX/Linux operating system and command line, including:

Objectives

After this workshop participants should be able to:

  • Use the Unix command-line as a tool for data analysis
  • Describe the different sequencing data file formats available
  • Perform QC assessment of high throughput sequencing data
  • Explain the algorithmic concepts behind read alignment, variant calling and structural variant detection
  • Perform read alignment, variant calling and structural variation detection using standard tools

 

Date

Module

Topic

Sessions

15 August

 

Welcome to the course

Get to know your classroom and meet your teaching assistants and fellow participants

17 August

Using Vula effectively and classroom bios

22 August

1

Introduction to Unix/Linux

Introduction to Linux command line tools

24 August

Introduction to Linux command line tools II

29 August

2

Introduction to sequencing technologies

Introduction to sequencing technologies

31 August

3

Sequencing data formats and QC

Data pre-processing and QC I

5 September

Data pre-processing and QC II

7 September

4

Alignment to Reference

Alignment to Reference

12 September

No session

14 September

5

Variant Calling - Human

Human Variant Calling

19 September

Human Variant Calling II Structural

21 September

6

Variant Calling - Pathogen

Science talks

26 September

Pathogen Variant Calling I

28 September

Pathogen Variant Calling II

3 October

 

Workshop and wrap up

FAIR and data sharing workshop

5 October

Course evaluation and wrap up

Workshop limitations
For more information, please visit
Training material availability
<p><span style="font-weight: 400;">Training materials for this course are currently being curated and disseminated but a git repository can be accessed here: <a href="https://github.com/WCSCourses/GSBAfrica2023">https://github.com/WCSCourses/GSBAfrica2023</a>;, in the interim.</span></p>