Oxford Nanopore releases Short Fragment Mode: a new tool for real-time sequencing of short fragments of DNA

Today Short Fragment Mode will be integrated into the operating software that drives nanopore devices, allowing sequencing of fragments as short as 20 bases on nanopore platforms.

Using nanopore technology, it’s possible to sequence short to ultra-long fragments of DNA. Recent developments in software have enabled Oxford Nanopore to “unlock” the ability to sequence the shortest of DNA fragments, down to 20 bases in length.

Following the MinKNOW 22.03 software release today, all customers will instantly gain access to the first release of Short Fragment Mode (SFM) at no extra cost. As the update is a result of software rather than chemistry updates, users will not require any new sequencing reagents or devices to reap the benefits of SFM .

Nanopore technology is designed to enable a user to sequence whatever DNA fragment length they present to the pore. Having already demonstrated sequencing reads greater than four megabases in length, nanopore sequencing is the only technology on the market capable of sequencing DNA lengths spanning five orders of magnitude in a single technology. From the single-use Flongle to the high-throughput PromethION, SFM will be available at the scale required for users to answer their most crucial biological questions.

Short Fragment Mode is also coupled with Oxford Nanopore’s ability to generate high outputs per flow cell (with over 250M reads demonstrated on a single PromethION flow cell) of information rich data. Users can now easily access methylation information of short molecules, such as cell free DNA, using the latest methylation detection tool Remora.

This latest release enables users to generate highly accurate information rich data on any molecule from 20 bases to millions of bases long using nanopore technology. The team look forward to working with the Nanopore Community to show the capability of this method to uncover new areas of biology.

Find out more about Short Fragment Mode