Realfreq: real-time base modification analysis for nanopore sequencing.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 40189895.
- Also identified by DOI 10.1093/bioinformatics/btaf151 and PMC identifier 12079415.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Nanopore sequencers allow sequencing data to be accessed in real-time. This allows live analysis to be performed, while the sequencing is running, reducing the turnaround time of the results. We introduce realfreq, a framework for obtaining real-time base modification frequencies while a nanopore sequencer is in operation. Realfreq calculates and allows access to the real-time base modification frequency results while the sequencer is running. We demonstrate that the data analysis rate with realfreq on a laptop computer can keep up with the output data rate of a nanopore MinION sequencer, while a desktop computer can keep up with a single PromethION 2 solo flowcell. Realfreq is a free and open-source application implemented in C programming language and shell scripts. The source code and the documentation for realfreq can be found at https://github.com/imsuneth/realfreq. The version used for the manuscript is also available at https://doi.org/10.5281/zenodo.15128668.
Medical subject headings
- Nanopore Sequencing
- Software
- Sequence Analysis, DNA
- Nanopores