Realfreq: real-time base modification analysis for nanopore sequencing

Oxford Nanopore Technologies generates sequencing data in real time and annotates with base modifications within the same run. Samarasinghe et al. introduce realfreq — a new tool for instant methylation calling. Live epigenetic analysis could aid time-sensitive clinical diagnostics and forensic investigations in the future.

Key points:

• Realfreq processes raw nanopore signal data and provides immediate access to methylation patterns on DNA or RNA.

• Realfreq kept up with the data output of a MinION Flow Cell on a laptop, and successfully maintained real-time processing over a 48-hour sequencing run on a PromethION Flow Cell using a desktop computer.

• Base and modification calling took ~87.3% of processing time, alignment took ~8.7%, and data conversion took ~2.4%.

• Realfreq is a free and open-source application on GitHub.

Sample type: DNA and RNA simulation datasets