Nanopore QC analysis

Quality control, Basecalling and multiplexing of sequencing reads generated by Oxford Nanopore sequencers.

As a routine we provide quality control and a few analyses available onboard the PromethION sequencing instrument.

The onboard software, MinKNOW, provides the following functions: 

• Basecalling, i.e. the computation of usable read sequence information from the Nanopore signal data.  
• From the Nanopore signal data from DNA we will by default generate (hydroxy-)methylation (5mC and 5hmC) calls in all contexts. For other DNA and RNA base modification calling options that are available, please see this document from Oxford Nanopore, or contact us. If you need some other configuration it’s important that you mention that when you place an order.
• When barcoding kits have been used to prep your samples to sequencing libraries, they will be demultiplexed onboard into separate folders.

As part of the data delivery you will receive a report generated by the MinKNOW software which details important QC metrics: sequence fragment lengths, quality score (Q) distributions and sequence yields of the flowcell and demuxed samples.

The raw data is delivered in (unmapped) uBAM files.

Last Updated: 11th December 2025