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.
F5N is the first ever Android application for nanopore sequence analysis on a mobile phone, comprised of popular tools for read alignment (Minimap2), sequence data manipulation (Samtools) and methylation calling (F5C/Nanopolish). On NA12878 nanopore data, F5N can perform a complete methylation calling pipeline on a mobile phone in ∼15 minutes for a batch of 4000 nanopore reads (∼34 megabases). F5N is not only a toolkit but also a framework for integrating existing C/C++ based command line tools to run on Android. F5N will enable performing nanopore sequence analysis on-site when used with an ultra-portable nanopore sequencer (eg: MinION or the anticipated smidgION), consequently reducing the cost for special computers and high-speed Internet.Availability and implementationF5N Android application is available on Google Play store at https://play.google.com/store/apps/details?id=com.mobilegenomics.genopo&hl=en and the source code is available on Github at https://github.com/SanojPunchihewa/f5n.Contacthirunas@eng.pdn.ac.lk
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