Short fragment mode

Nanopore technology enables the sequencing of short to ultra long DNA or RNA fragments, providing a universal sequencing platform capable of observing the full scope of biology

One platform

One technology, one platform for all your biology​

Following recent developments in chemistry and software, Oxford Nanopore has now “unlocked” the ability to sequence the shortest of DNA fragments on our platform, down to 20 bases in length. We call this Short Fragment Mode (SFM)​.

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, requiring no extra instruments or sample preparation methods.​ ​

With options from the single-use Flongle to the high-throughput, high-yield PromethION, we anticipate our users will be able to satisfy their needs regardless of scale or application, and ultimately arrive at the most important answer — the one for their specific biological question.

Figure 1: Choose your read length cut off using the Minimum Read Length filter within MinKNOW

Figure 2. A DNA ladder is run with 2 different minimum read length settings: A) 200 bp and B) 20 bp. With a setting of 20 bp, fragments below 200 bases in length are recorded for further analysis.

How it works

How it works

​SFM is enabled by a new configuration setting in MinKNOW (first released to the Nanopore Community in March 2022 — see Figure 1). During run setup a user simply selects their preferred minimum read length.

The setting is used to direct the software to write sequencing files to disk from the minimum size selected. The performance of this is demonstrated in Figure 2, with the experimental outputs of running a DNA ladder with the minimum length set to A) 200 bp and B) 20 bp shown — the read length distribution matches the chosen software setting.



SFM will enable the community to deploy nanopore sequencing for use in exciting areas such as liquid biopsy research, sequencing of FFPE samples, or cell-free DNA analysis. At London Calling 2022 the CTO of Oxford Nanopore, Clive Brown, shared the sequencing of his own cell-free DNA (the CliveOME cfDNA dataset). Biology including plausible tissue typing via methylation data and insight into nucleosome rearrangement was uncovered — hear more about that in this short video.

Users will be able to pair SFM with other nanopore capabilities such as highly scalable outputs, amplification-bias free workflows, and the detection of methylation without additional preparation.​

We'd love to hear your ideas, so please follow the link below to leave us feedback on the applications you would like to pursue with SFM.


Give us your feedback

We always want to have our customers' input at the heart of what we do and the products we develop. We're incredibly excited about the introduction of SFM, and we'd love to hear your ideas on where this new feature can be applied.

Please click the button below to submit your thoughts, ideas, and improvements for SFM.

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