Course Overview
Next generation sequencing (NGS) 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 next generation sequencers. This course will equip participants with the essential informatics skills required to begin analysing NGS data and apply some of the most commonly used tools and resources for sequence data analysis. The programme will cover 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 - QC, alignment, assembly, variant calling and RNA-Seq.
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 next generation sequencing data analysis.
Keywords: NGS, Data analysis, Genomics, Sequence analysis
Skill level of training: Intermediate
Language: English
Credential awarded: Certificate of attendance/completion
Type of training: Blended/hybrid learning
Venue of the course: Virtual format (Zoom)
Dates for the course: Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT
Course organisers: Wellcome Genome Campus/ Wellcome Connecting Science and H3ABioNet
Participation: N/Applicants should be postdoctoral scientists, senior PhD students, junior faculty members or clinicians/healthcare professionals actively engaged in or soon to commence research involving next generation sequencing data analysis. Priority will be given to applicants who 1) currently or will soon have NGS experimental data to analyse 2) will utilise the bioinformatics techniques taught in at least two of the modules/topic areas listed in the programme outline in their experiments 3) have a clear plan/opportunity to disseminate the knowledge amongst their peers. We encourage applicants to highlight these areas in their application.
Course Sponsors: Wellcome Genome Campus/ Wellcome Connecting Science and H3ABioNet
Course objectives

After this workshop participants should be able to:

• Use the unix command-line as a tool for data analysis
• Describe the different NGS 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
• Analyse RNA-Seq and CHiP-seq data
• Perform a genome assembly using NGS data 

 

Classroom applications

Registration for classrooms opens: Thu, 01/01/1970
Registration for classrooms closes: Thu, 01/01/1970
Link to classroom application form:
Notification date for successful classrooms: Thu, 01/01/1970
Maximum number of participants that may be accepted per classroom will be capped at 40

Participant applications

Registration for participants opens: Thu, 01/01/1970
Registration for participants closes: Thu, 01/01/1970
Participant registration link:

Syllabus and Tools

The course will cover the following topics:

• Intro to Unix/Linux & running workflows
• Introduction to NGS Technologies
• NGS data pre-processing and QC
• Alignment to reference sequences
• Variant calling and annotation
• ChipSeq
• RNASeq
• Genome assembly

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:

Course limitations
The course aims to provide a hands-on introduction to bioinformatics for next generation sequencing, and should not be considered a complete education in the theoretical and mathematical foundations of the topics.
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/NGS_Bio_Africa">https://github.com/WCSCourses/NGS_Bio_Africa</a>;, in the interim.</span></p>