1. Genopo: a nanopore sequencing analysis toolkit for portable Android devices.
- Author
-
Samarakoon H, Punchihewa S, Senanayake A, Hammond JM, Stevanovski I, Ferguson JM, Ragel R, Gamaarachchi H, and Deveson IW
- Subjects
- Betacoronavirus pathogenicity, COVID-19, Cell Phone instrumentation, Computational Biology instrumentation, Coronavirus Infections diagnosis, Coronavirus Infections virology, DNA Methylation, High-Throughput Nucleotide Sequencing instrumentation, Humans, Nanopores, Pandemics, Pneumonia, Viral diagnosis, Pneumonia, Viral virology, SARS-CoV-2, Whole Genome Sequencing instrumentation, Betacoronavirus genetics, Computational Biology methods, Genome, Human, Genome, Viral, High-Throughput Nucleotide Sequencing methods, Whole Genome Sequencing methods
- Abstract
The advent of portable nanopore sequencing devices has enabled DNA and RNA sequencing to be performed in the field or the clinic. However, advances in in situ genomics require parallel development of portable, offline solutions for the computational analysis of sequencing data. Here we introduce Genopo, a mobile toolkit for nanopore sequencing analysis. Genopo compacts popular bioinformatics tools to an Android application, enabling fully portable computation. To demonstrate its utility for in situ genome analysis, we use Genopo to determine the complete genome sequence of the human coronavirus SARS-CoV-2 in nine patient isolates sequenced on a nanopore device, with Genopo executing this workflow in less than 30 min per sample on a range of popular smartphones. We further show how Genopo can be used to profile DNA methylation in a human genome sample, illustrating a flexible, efficient architecture that is suitable to run many popular bioinformatics tools and accommodate small or large genomes. As the first ever smartphone application for nanopore sequencing analysis, Genopo enables the genomics community to harness this cheap, ubiquitous computational resource.
- Published
- 2020
- Full Text
- View/download PDF