SeqAfrica Resources

Recordings and training material from these courses are Freely Available on each course page

Resources for ONT sequencing - Protocols

SeqAfrica has developed a protocol packet for sentinel surveillance sires to use in Oxford Nanopore Technology (ONT) sequencing and analysis. The packet contains a series of user-friendly protocols developed to go from bacterial sample to completed analysis using ONT and desktop-based analysis software.

SeqAfrica GitHub Page

This GitHub page hosts multiple repositories created by the SeqAfrica project, featuring bioinformatics training materials, datasets, exercise files, hackathon resources, and code for workflows and pipelines supporting AMR surveillance and bacterial genomics. You can also access our comprehensive 4-day AMR and bioinformatics training curriculum in the zimbabwe-course repository.

SeqAfrica Bioinformatic Community of Practise

Join our monthly meet-up for everyone passionate about bioinformatics. Each session features a stand-up round where participants share their current projects, followed by a "Soapbox" segment showcasing scientific talks, tool demonstrations, or discussions of new developments in the field. This relaxed and interactive space encourages questions, tips, and idea sharing. Meetings are held on Zoom the first Thursday of every month from 12:30 to 13:15 CEST. To receive an invitation, email pnil@food.dtu.dk. Additionally, our community maintains a traditional mailing list for submitting questions, sharing links to tools and manuscripts, and more. To join the mailing list, send an empty email to bioinfo-list-join@seqshare.org.

Whole genome sequencing of bacterial genomes - tools and applications

This Coursera course provides an in-depth understanding of Whole Genome Sequencing (WGS) and its applications in bacterial research and surveillance. Through short video lectures, participants will learn about bacterial subtyping and the use of next-generation sequencing technology for research and monitoring. The course includes demonstrations and guided exercises on using online tools for bioinformatic analysis, enabling learners to conduct basic bioinformatic tasks. Ideal for students, researchers, and professionals in the medical and biological sciences, this course equips participants with the skills to apply WGS in various contexts, including species identification, antimicrobial resistance characterization, and plasmid typing.

Antimicrobial resistance - theory and methods

This Coursera course offers comprehensive insights into antimicrobial resistance (AMR), an increasingly pressing global concern. Through short video lectures, participants will explore fundamental topics such as basic definitions and an overview of antimicrobials and their effects, mechanisms of antimicrobial action, and the selection and dissemination of antimicrobial resistance. Additionally, the course includes a module on antimicrobial susceptibility testing methods and the use of genomic tools for analysing Whole Genome Sequencing data to detect resistance genes and other genes of interest. Ideal for students, researchers, healthcare professionals, and laboratory technicians, this course equips learners with the theoretical and practical skills necessary for identifying and testing AMR.

Introduction to WGS in AMR surveillance

This course is an introduction to Whole Genome Sequencing (WGS) and its use in AMR surveillance for those who would like to know more about why it is important and how can it can be incorporated.

Click below to read more and find resources and recordings.

WGS workflow - from isolate to analysis

This course is to be considered a continuation of Introduction to WGS in AMR. Here the entire workflow, from sampled isolate to finished analysis of sequencing data will be covered in lectures and hands-on exercises.

Click to read more and find resources for participants.

Simulation Exercises

The SeqAfrica project invites Fleming Fund Fellows and Fleming Fund Country Grant participants to join a training workshop on an AMR outbreak detection using simulation exercises and genomic tools.

Click to read more and find resources for participants.

Basic bioinformatics using command line

This page provides an overview of available online courses that cover basic bioinformatics and is well suited for those who would like to move from using online tools to command line tools to increase their analysis throughput.

Click to read more and find resources for participants.

SARS-CoV-2 - whole genome sequencing

SeqAfrica Whole Genome Sequencing Webinar Series

The SeqAfrica project invited experts from organizations across the globe to share their expertise on how to select isolates for sequencing, how to choose and collect the right metadata for your sequencing work, and how to communicate your sequencing results.

Click here to watch the webinar recordings.

Minimum metadata that should be submitted with all WGS requests.

Sample shipping guidance

This guide describes sample preparations and shipping guidelines for clients receiving Whole Genome Sequencing services by SeqAfrica. It covers recommendations and guidance on shipping bacterial isolates or extracted DNA to the sequencing centres for short-read sequencing.

Read the Guidance here.