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index.qmd
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# About {.unnumbered}
Welcome to the Pathogen Genomics Module of the FA5 Bioinformatics course, created by the [Institute of Tropical Medicine Antwerp](https://www.itg.be/en/) (ITM) in collaboration with the [University of Antwerp](https://www.uantwerpen.be/en/). Its primary goal is to support the implementation of sequencing bioinformatics to strengthen molecular surveillance and pathogen research.
## Scope of the course
This course aims to provide an overview of the key bioinformatics concepts related to performing pathogen genomics. It is divided into the following sections:
1. Introduction to the Unix shell
2. Processing genomics data
## Computational thinking
We hope that this course can teach you a few computational thinking and problem solving skills that will help you along your bioinformatics journey. The learning curve in computational biology can be quite steep at times and the path is littered with arcane commands and obtuse syntax, but as you practice the concepts introduced in this course on your own, your command-line efficiency will improve and you will start to spot similarities across different types of environments and languages. Through this course, we hope to arm you with the necessary skills to make tasks like running custom analysis scripts or installing bioinformatics software seem a little less daunting, and enough knowledge and experience to be able to explore more advanced topics on your own.
# Acknowledgements {.unnumbered}
<!-- This course was made possible thanks to the support of [VLIR-UOS](https://www.vliruos.be) and the [Institute of Tropical Medicine](https://www.itg.be/en). -->
Development of the original version of this course (see https://pmoris.github.io/FiMAB-bioinformatics/) was supported by [VLIR-UOS](https://www.vliruos.be), the [Institute of Tropical Medicine (ITM)](https://www.itg.be/en), and the [University of Antwerp](https://www.uantwerpen.be/en/).
This version of the course was developed within the FA5 program of ITM, and with support of the Adrem Data Lab at the University of Antwerp.
About FA5: The Alliance for Education in Tropical Medicine and International Public Health, part of the FA5 agreement between ITM and the DGD (Directorate-General for Development Cooperation and Humanitarian Aid of the Belgian government), focuses on building educational partnerships and fostering collaboration with international higher education institutions in FA5 countries and beyond. Its main goal is to enhance quality, innovation, internationalization, and peer learning in postgraduate education, with mutual learning at its core. More info via [this link](https://www.itg.be/en/study/collaboration).
# License [{fig-alt="CC" height=30px}](https://creativecommons.org/licenses/by/4.0/) [{fig-alt="BY" height=30px}](https://creativecommons.org/licenses/by/4.0/) {.unnumbered}
This work is licensed under the [Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0/).
This (loosely-speaking) means that you are free to copy, redistribute or adapt any of its contents, provided that you **do** reference us and the original license, **do** indicate if modifications were made, **do** distribute those contributions under the same license and **do not** use the material for commercial purposes.