amr
Welcome to the AMR Analysis Pipeline Guide
Antimicrobial Resistance (AMR) poses a significant challenge to global health, rendering many standard treatments ineffective against bacterial infections. Understanding and identifying AMR mechanisms are crucial steps toward combating this issue. This guide is designed to demystify the process of analyzing sequencing data to detect AMR genes, making it accessible even to those without prior experience in bioinformatics or Linux systems.
Who Is This Guide For?
Whether you’re a molecular biologist, a clinician, a researcher, or simply someone interested in understanding how AMR is detected and analyzed, this guide offers a comprehensive walkthrough. No prior experience with Linux or bioinformatics pipelines is required.
What Will You Learn?
- DNA Sequencing Platforms: Gain insights into both short-read (e.g., Illumina, MGI) and long-read (e.g., Oxford Nanopore Technology, Pacific Biosciences) sequencing technologies, understanding their applications and limitations.
- Introduction to Linux: Learn the basics of the Linux operating system, its importance in bioinformatics, and how to set up a Linux-like environment on Windows using WSL2.
- Bioinformatics Pipeline: Step-by-step guidance through the processes of quality checking, assembling, and annotating sequencing data to identify AMR genes.
Why Focus on AMR?
The rise of AMR threatens the effectiveness of antibiotics, making infections harder to treat and increasing the risk of disease spread, severe illness, and death. By understanding and identifying resistance genes through sequencing data, we can better monitor, prevent, and control the spread of resistant pathogens.
How to Navigate This Guide
Each section is structured to build upon the previous one, starting with foundational knowledge and progressing to more advanced topics. Practical examples, visual aids, and links to additional resources are provided to enhance your learning experience.
Get Started
Lets start from the first page of Introduction to AMR Analysis Pipeline.
Note: This guide is continually updated to reflect the latest advancements in sequencing technologies and AMR analysis methodologies.
This works is enabled by the support from The UK aid Fleming Fund Country Grant to Indonesia Phase II.