Course Overview/description: 

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.

This course will apply a blended learning format consisting of locally coordinated classrooms referred to as “remote classrooms”. Click here for more information. Please note: Due to the COVID-19 pandemic, the local classrooms will likely run virtually, using Zoom and downloadable virtual machines.

Would you like to enroll in the course in 2022?

Please apply to take the course by clicking here

Applications close 21 February 2022 at midnight (CAT)

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.

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.

Learning objectives/outcomes: 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 

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:

• http://www.ee.surrey.ac.uk/Teaching/Unix
• http://swcarpentry.github.io/shell-novice/

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

Dates for the workshop:

Tuesdays & Thursdays from 22/03/2022 until 20/06/2022 (staff training will happen ahead of this)

Classroom registration opens:

03/12/2021

Classroom registration closes:

10/01/2022

Notification date:

17/01/2022 

Participant applications:

Applications are now open and will close on 21 February at midnight (CAT).  Apply here.

Workshop organisers:

WGC WCS and H3ABioNet

Workshop Sponsors:

Wellcome Genome Campus/ Wellcome Connecting Science and H3ABioNet 

Keywords:

NGS, Data analysis, Genomics, Sequence analysis

Skill level of training:

Advanced 

Language:

English 

Credential awarded:

Letter of completion

Type of training:

Likely to be run in a virtual format

Workshop 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.

Workshop Programme:

The workshop will run for ~10 weeks, on Tuesdays and Thursdays from the 22nd of March until the 20th of June. 

Please apply to take the course by clicking here

Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources.

Intended Audience: The course is aimed at individuals from a molecular biology background who have a basic understanding of biochemistry and/or genetics and would like to become bioinformatics users. For an explanation on who 'bioinformatics users' might be, see Figure 2 in http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003496. A baseline level of the understanding of the central dogma of biology (DNA -> RNA -> Protein) is a requirement.

Keywords: Genetics, Genomics, Nucleic acids analysis

Skill level of training: Beginner

Language: English

Credential awarded: Letter of completion

Type of training: Blended/hybrid learning

Logistics 

Venue of workshop: Local classrooms ( usually ~40 physical/online sites across Africa). Please be aware that the course is likely to make use of a combination of both physical and online sites depending on ongoing Covid-19 restrictions.

Dates for the workshop: 06 July – 12 October 2021; Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT.

Workshop organisers: Paballo Chauke, Verena Ras, Shaun Aron, Sumir Panji and Nicola Mulder

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: H3ABioNet + Local Classrooms

Classroom applications:

Registration for classrooms opens:  26 April 2021

Registration for classrooms closes: 11 May 2021

Link to classroom application form: <Classroom registration is now closed> 

Notification date for successful classrooms: 19 May 2021

Participant applications:

Registration for participants opens:  20 May 2021

Registration for participants closes: 14 June 2021 at 11:59 pm CAT

Application instructions: Participants must select a classroom within their region and that they are able to attend physically should that particular classroom choose to go ahead as a face-to-face classroom. Please be sure to adhere to this as selecting a classroom outside of your region/location may result in your application being rejected. Please also be aware that applying for the course does not guarantee entry - you will undergo a formal selection process.

Click here to apply!

Syllabus and Tools:

The course curriculum will cover the following main themes (subject to slight changes):

• Bioinformatics resources and databases
  • Introduction to bioinformatics, biological databases and resources (NCBI and EBI), data formats, ontologies
• Linux
  • Introduction to Linux, general overview of Linux environment, overview of command line interface, navigating Linux directory structure, manipulating files and directories, basic Linux commands
• Sequence alignment theory and applications
  • Introduction to searching and sequence alignment, BLAST, pairwise sequence alignment
• Multiple sequence alignment (MSA)
  • MSA theory, generating and interpreting MSAs using various tools, visualising and assessing MSA quality
• Genomics
  • Overview of sequencing and annotation, Ensembl genome browser, Genetic variation, HapMap, 1000 genomes
• Molecular evolution and phylogenetics
  • Molecular evolution, phylogenetic approaches and methods (Introduction and overview of methods)

 **All modules make use of predominantly web-based tools such as NCBI, Ensembl, etc.

Prerequisites: A basic background/understanding of of biochemistry and/or genetics.

Objectives: After this workshop participants should be able to:

• Explain the use of bioinformatics
• Name the key bioinformatics techniques and tools
• Locate important biological databases and retrieve data
• Use selected tools effectively to run specific bioinformatics analyses
• Understand the strengths and limitations of the various techniques

Workshop limitations: This workshop will only provide a foundation for continued learning in bioinformatics and will not teach any advanced coding.

Training Material Availability:

Training materials for this course are available here: https://zivahub.uct.ac.za/projects/Introduction_to_Bioinformatics_Training_Course_Materials/131552. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

Materials have been made available as a single archive per module containing lecture slides, transcribed videos, practical assignments and any other resources important to complete each module:

Module 1: Databases and Resources

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_1_Databases_and_Resources_Training_Material_Archive/19106741 

Module 2: Linux

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_2_Linux_Training_Material_Archive/19106744 

Module 3: Sequence Alignment

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_3_Sequence_alignment_Training_Material_Archive/19106750 

Module 4: Multiple Sequence Alignment

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_4_Multiple_Sequence_Alignment/19106759 

Module 5: Genomics

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_5_Genomics/19106762 

Module 6: Phylogenetics (2018 - 2021)

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_6_Phylogenetics/19106765 

Module 6: Structural Biology (2016 only)

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_6_2016_Structural_Biology/19129892 

Introduction Week

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_-_Introduction_Week_Training_Material_Archive/19106738 

Wrap Up week

•  https://zivahub.uct.ac.za/articles/educational_resource/Wrap_up_Week/19106768 

For more information on IBT, please visit: https://www.h3abionet.org/training/ibt

Course Overview:  The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will provide training to enable participants to gain the knowledge and skills to perform 16S rRNA microbiome data analyses using a variety of bioinformatics methods and tools.

The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will use a blended learning approach similar to the popular H3ABioNet Introduction to Bioinformatics Training (IBT) through the use of a combination of theoretical and practical sessions in order for participants to gain knowledge in the use of various tools and resources needed for 16S rRNA microbiome data analysis. There will be 2 contact sessions per week consisting of both theoretical and practical coursework. Participants will generally watch pre-recorded videos (theory) followed by a practical exercise for the remainder of the session. Contact sessions will generally be 4 hours each however the exact format and length of classes will be communicated in due course. 

Intended Audience: Anyone who will be working with 16S rRNA microbiome data and would like to learn more about the bioinformatics analyses.

Keywords: 16S, Microbiome, NGS, Genomics, Nucleic acid analysis

Language: English

Skill level: Intermediate

Type of training: Blended/hybrid learning

Credential awarded: Letter of completion

Dates for the Course: 28 September to 23 November 2021 (participants will join on 05 October 2021)

Venue of the Course: Successful hosting classrooms

Course Organizers: Verena Ras, Gerrit Botha, Shaun Aron, Sumir Panji, Nicola Mulder

Course Objectives (TBC): By the end of the course participants should be able to:

• Describe the importance of the microbiome and why it should be studied
• Understand how to design 16S rRNA microbiome studies
• Be able to apply basic syntax and operations in R
• Understand the different NGS data types (e.g. MiSeq reads) produced for a 16S rRNA microbiome study
• Evaluate the quality of NGS sequence reads and samples
• Understand the various bioinformatics tools used for 16S microbiome studies
• Understand the various 16S rRNA bioinformatics pipelines being used to study the microbiome.
• Apply the H3ABioNet’s 16S rRNA pipeline and understand how to execute this
• Understand the use of workflow languages (Nextflow) and containerized images (Singularity) to automate analyses
• Analyze 16S rRNA microbiome data and interpret results

Syllabus and Tools (TBC):

• Introduction to the Linux command line / intro to R
• Introduction to the microbiome and study design – why 16S?
• Sample collection, extraction and library prep for 16S NGS analyses
• 16S rRNA gene amplicon sequencing bioinformatics pipeline: the theory
• 16S analysis pipeline - QC, ASV picking, taxonomic classification and alignment
• Downstream analysis in R - using the packages phyloseq, NMF, vegan, metagenomeSeq (among others)

Prerequisites (for participants): As this is an intermediate course, some familiarity with the Unix command line and R scripting will be assumed. However, should participants wish to gain some background knowledge before the start of the course, the following tutorials will provide a good foundation. 

Linux: http://www.ee.surrey.ac.uk/Teaching/Unix/

R: https://www.statmethods.net/r-tutorial/index.html

R: https://www.datacamp.com/courses/free-introduction-to-r 

Workshop limitations: This workshop provides an overview and guidance on 16S rRNA microbiome analyses and will provide you with the ability to perform a variety of analyses on microbiome data. The course however will not teach any advanced programming or go into depth with R or Unix. Participants are encouraged to explore these tools in greater depth independently.

Training Materials Availability:

Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19106780. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

Click here to access the general course site