Genopo

Genopo performs on-device analysis of Oxford Nanopore sequencing data on Android smartphones, enabling read alignment, sequence data manipulation, and methylation calling for nanopore datasets using established command-line tools.

Key Features:

• Integration with Popular Tools: Integrates Minimap2 for read alignment, Samtools for sequence data manipulation, and F5C/Nanopolish for methylation calling on nanopore data.
• Methylation Calling Pipeline: Executes a complete methylation calling pipeline on nanopore sequencing data and processed approximately 4,000 reads (~34 megabases) of the NA12878 dataset in about 15 minutes.
• Framework for C/C++ Tools: Provides a framework to compile and execute existing C/C++ command-line genomics tools on Android platforms.
• Compatibility with Nanopore Devices: Supports data processing from ultra-portable Oxford Nanopore sequencers such as MinION and smidgION for on-site or real-time analysis.

Scientific Applications:

• Field-based nanopore sequencing: Enables on-site processing of nanopore sequencing data for fieldwork or remote locations with limited laboratory infrastructure or internet connectivity.
• On-device methylation analysis: Allows rapid methylation calling directly from nanopore sequencing runs for studies requiring immediate epigenetic insight.

Methodology:

Integrates and executes command-line tools (Minimap2, Samtools, F5C/Nanopolish) within an Android environment, implements a methylation calling pipeline on nanopore reads, and provides a framework for running C/C++ command-line genomics tools with data from devices such as MinION and smidgION.