Nanopore Sequencing Analysis App Enables Fully Portable Computation

Portable nanopore devices exist that enable scientists to sequence the genetic material in a biological sample outside a laboratory, however analyzing the raw data has still required access to high-end computing power. A new mobile app called Genopo, developed by the Garvan Institute of Medical Research in collaboration with the University of Peradeniya in Sri Lanka, attempts to remedy that shortcoming and make genomics more accessible to remote or under-resourced regions, as well as the hospital bedside.

"Fast, real-time genomic analysis is more crucial today than ever, as a central method for tracking the spread of coronavirus. Our app makes genomic analysis more accessible, literally placing the technology into the pockets of scientists around the world,” explains Ira Deveson, co-senior author of a paper published today in Communications Biology that describes the nanopore sequencing analysis toolkit.

To enable in situ genomic sequencing and analysis, in real time and without major laboratory infrastructure, we developed an app that could execute bioinformatics workflows on nanopore sequencing datasets that are downloaded to a smartphone. The reengineering process, spearheaded by first author Hiruna Samarakoon, required overcoming a number of technical challenges due to various resource constraints in smartphones. The app Genopo combines a number of available bioinformatics tools into a single Android application, miniaturized to work on the processing power of a consumer Android device.

The researchers tested Genopo on the raw sequencing data of virus samples isolated from nine Sydney patients infected with SARS-CoV-2, which involved extracting and amplifying the virus RNA from a swab sample, sequencing the amplified DNA with a MinION device and analyzing the data on a smartphone. The researchers tested their app on different Android devices, including models from Nokia, Huawei, LG and Sony.

The Genopo app took an average 27 minutes to determine the complete SARS-CoV-2 genome sequence from the raw data, which the researchers say opens the possibility to do genomic analysis at the point of care, in real time. The researchers also showed that Genopo can be used to profile DNA methylation in a sample of the human genome.

"This illustrates a flexible, efficient architecture that is suitable to run many popular bioinformatics tools and accommodate small or large genomes," says Dr Deveson. "We hope this will make genomics much more accessible to researchers to unlock the information in DNA or RNA to the benefit of human health, including in the current pandemic."

Genopo is a free, open-source application available through the Google Play store.