Efficient real-time selective genome sequencing on resource-constrained devices.

ABSTRACT:

Background

Third-generation nanopore sequencers offer selective sequencing or "Read Until" that allows genomic reads to be analyzed in real time and abandoned halfway if not belonging to a genomic region of "interest." This selective sequencing opens the door to important applications such as rapid and low-cost genetic tests. The latency in analyzing should be as low as possible for selective sequencing to be effective so that unnecessary reads can be rejected as early as possible. However, existing methods that employ a subsequence dynamic time warping (sDTW) algorithm for this problem are too computationally intensive that a massive workstation with dozens of CPU cores still struggles to keep up with the data rate of a mobile phone-sized MinION sequencer.

Results

In this a

SUBMITTER: Shih PJ 

PROVIDER: S-EPMC10316692 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature