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Dynamic Adaptive Sampling in Nanopore Sequencing

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  • Dynamic Adaptive Sampling in Nanopore Sequencing

    Researchers from EMBL’s European Bioinformatics Institute (EMBL-EBI) and the University of Nottingham have implemented a new method for adaptive sampling in nanopore sequencing.

    Their work, recently published in Nature Biotechnology, builds upon nanopore sequencing’s ability to reject unwanted DNA molecules after a brief analysis. Adaptive sampling, also known as “read until”, is a process that allows users to select the specific DNA fragments they wish to sequence.

    The new method, BOSS-RUNS (Benefit-Optimizing Short-term Strategy for Read Until Nanopore Sequencing), utilizes different algorithms to optimize the rate of information gain during resequencing and improve adaptive sampling. BOSS-RUNS is an open-source software that enables researchers to optimize their protocols and adjust them to fit their needs.

    Data from the study shows that BOSS-RUNS can be used to dynamically change targets during sequencing, leading to increased sequencing yields of on-target regions and improved variant calling.

    This approach to adaptive sampling is advantageous when sequencing multiple genomes concurrently, such as in mixed microbial communities. BOSS-RUNS can be used to prevent redundant DNA from being sequenced and ensure each species can receive sufficient coverage.

    The details for implementing BOSS-RUNS are available for use on GitHub.

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