Hey there, this is Alex Barquero from the RuizLAB team, and I’m happy to share our journey in creating the first Android app for nanopore sequencing analysis: KARGAMobile. This app is a demonstration of the possibilities that exist in the fight against antimicrobial resistance (AMR), providing users with a portable, real-time, and easily interpretable solution for identifying antibiotic resistance genes (ARGs) from nanopore sequencing data directly from their Android devices. In this post, I will also share a video which highlights some of the features that we created for KARGAMobile.
Confronting the Challenge
Nanopore sequencing is a powerful microbial analysis mechanism, but there is a significant challenge when it comes to the amount of data and the processing power it requires to work adequately. In regions with limited internet connectivity, transferring large amounts of data to high-performance servers for processing is impractical. For this reason, we set out to develop an app that could perform all the necessary computations right on the mobile device, eliminating the need for data transfer.
Designing a user-friendly graphical interface for KARGAMobile was no small feat. We embarked on a meticulous process, starting with paper prototypes and wireframes to ensure a smooth and intuitive user experience, within the screen real estate limitations of a mobile device. Our goal was to make the app accessible to all possible users, be it public health officials, healthcare providers, and researchers alike.
As an example of one of the multiple features, the system allows users to customize ARG analysis parameters and select input files with ease. Through Android’s file picker system, users can choose the input read and reference database files that suit their specific needs.
Optimizing Performance for Mobile Devices
To optimize the app for mobile devices, we built KARGAMobile on the Java code of the pre-existing KARGA tool. However, we didn’t stop there. We made crucial adjustments, such as using an in-memory database, compressing the ARG reference database, and implementing data structures suitable for low RAM usage. The result? Constant memory usage, regardless of input file size or read size, which makes KARGAMobile practical on a wide range of Android devices.
Validation and Future Perspectives
Ensuring the accuracy of KARGAMobile was of importance to us. We conducted validation tests using semi-synthetic datasets and real experimental Nanopore data, comparing our app’s performance to the original KARGA tool. The outcome was satisfactory, since KARGAMobile achieved high accuracy and low false positive rates, confirming it to be a reliable tool for detecting ARGs while running on the edge in a mobile device.
The future looks bright for KARGAMobile. We’re committed to continually improving the app’s performance and usefulness and the users’ interactivity experience, as well as striving to reduce memory usage and enhance its overall efficiency.
Empowering the Fight Against AMR
Creating KARGAMobile has been a fun journey, knowing that our efforts will positively impact public health, especially in resource-limited environments. With KARGAMobile, it has been demonstrated that mobile devices can now independently perform real-time analysis of ARGs, transforming them into a powerful tool in the battle against antimicrobial resistance.
We extend our gratitude to our team members, collaborators, and everyone who supported us throughout this process.
If you’d like to learn more about KARGAMobile and its capabilities, please check out the full paper titled “KARGAMobile: Android app for portable, real-time, easily interpretable analysis of antibiotic resistance genes via nanopore sequencing”, which can be accessed in the following link.
Thank you for joining us on this journey, and we can’t wait to share more advancements with you in the future. Stay tuned!