SeqAfrica Resources

These genomic analysis tools support species identification, strain typing, antimicrobial resistance detection, and comparison of closely related bacterial genomes. Together, they enable users to analyze sequencing data for research, surveillance, and outbreak investigation purposes.

This guidance document provides practical recommendations for the safe preparation, packaging, documentation, and shipment of bacterial isolates or extracted genomic DNA for whole genome sequencing (WGS). Developed under the SeqAfrica project, it covers key considerations such as contamination prevention, labelling, transport media, quality control, and the relative advantages and limitations of shipping isolates versus extracted DNA. Although originally produced to support sample submission within SeqAfrica, this resource remains broadly relevant and can be used by laboratories as a general reference when shipping DNA or bacterial isolates to sequencing facilities or collaborating laboratories. The guidance is applicable across human, animal, and environmental sectors and is intended to support good laboratory practice and data quality during sample transport.

This Excel-based metadata template supports laboratories submitting bacterial isolates for whole genome sequencing (WGS) by helping ensure that a minimum, standardized set of epidemiologically relevant metadata is collected alongside sequencing data. The template covers key isolate, sampling, patient/host, location, and antimicrobial susceptibility testing (AST) information, distinguishing between mandatory fields and optional data that may be required for specific analyses. By using this template, laboratories can improve the epidemiological value, comparability, and downstream usability of their WGS data for national, regional, and international AMR surveillance, including One Health analyses across human, animal, and environmental sectors. The file also includes an example sheet with completed entries to guide users in filling in the metadata correctly.

This step by step guide provides a tested and reliable workflow for setting up an Ubuntu based laptop for Oxford Nanopore Technologies (ONT) sequencing analysis. It covers recommended hardware, Ubuntu installation, Nvidia driver setup, and the full ONT software stack, including MinKNOW, Dorado, Flye, and Medaka, along with guidance on Conda environments, Docker/Podman configuration, GPU enabled containers, and optional tools such as Nextflow. The manual incorporates practical fixes, troubleshooting tips, and notes on known ONT software quirks, making it a comprehensive reference for preparing robust, analysis ready laptops in laboratories.

This resource provides a comprehensive, hands on introduction to using the Linux command line for bioinformatics. Designed for learners with little or no prior experience, the course covers essential Linux skills, remote computing, shell scripting, and key approaches for installing and managing bioinformatics software. It further introduces core bioinformatics tools and workflows, including the CGE Tools/Bacterial Analysis Pipeline (BAP), and offers beginner friendly modules on bash scripting, Python, and R for data analysis.
This makes it a practical starting point for researchers and laboratory staff aiming to build command line confidence and strengthen their capacity in workflow-based genomic analysis.

This Excel file enables users to perform calculations and supports the determination of sample volumes for implementing ONT protocols

A generalized curriculum and agenda for a beginner-to-intermediate bioinformatics training that could be adapted for use by others.

Whole genome sequencing in AMR surveillance covers the fundamental principles of whole genome sequencing (WGS) and highlights the growing importance of WGS data in providing important policy-relevant insights for AMR surveillance. The course explores why, when and how WGS should be used as part of AMR surveillance, and supports learners to make a compelling case for utilising sequencing hubs or acquiring the necessary equipment to enhance WGS capacity.

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.

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.

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.

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.

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.

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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.

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 to read more and find resources and recordings.

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.