Introduction to live basecalling in MinKNOW
For MinION Mk1B and Flongle (on MinION Mk1B), the MinKNOW software presents an option to basecall reads on the local computer. The basecalling is carried out live, as the read files are generated during a sequencing experiment.
Basecalling results are displayed in real-time in the MinKNOW user interface, and data is written out in the BAM or FASTQ file format.
The MinION Mk1C, GridION and PromethION devices have the capacity to perform live basecalling, while keeping up with one (MinION Mk1C), five (GridION) and up to 41 flow cells (on the PromethION 48, or 48 flow cells on PromethION 48 A100) running fast basecalling simultaneously. Basecalling is carried out directly on the device and uses the MinKNOW software. The basecalled reads are written to the device; users can then export the reads out for further analysis via the Network or removable storage.
Fast, High Accuracy and Super Accurate models and compatibilities
The Dorado basecallers offer three different basecalling models: a Fast model, a High accuracy (HAC) model, and Super accurate (SUP) model.
The Fast model is designed to keep up with data generation on Oxford Nanopore devices (MinION Mk1C, GridION, PromethION). The HAC model provides a higher raw read accuracy than the Fast model and is more computationally-intensive. The Super accurate model has an even higher raw read accuracy, and is even more intensive than the HAC model.
For more information about basecalling accuracy, please consult the Accuracy page on the Oxford Nanopore website.
A comparison of the speed of the models is provided in the table below:
The number of keep-up flow cells assumes a 30 Gbase flow cell output in 72 hours for MinION and GridION, and 150 Gbase output in 72 hours for PromethION.
Sources of basecalling error
There are two main errors an event detection algorithm can make:
- Insertions: when an extra base is inserted where there should not be one - typically, this means a span of raw data points that corresponds to a single set of pore contents.
- Deletions: when a base is missed out.