ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing.

ABSTRACT: Nanopore selective sequencing allows the targeted sequencing of DNA of interest using computational approaches rather than experimental methods such as targeted multiplex polymerase chain reaction or hybridization capture. Compared to sequence-alignment strategies, deep learning (DL) models for classifying target and nontarget DNA provide large speed advantages. However, the relatively low accuracy of these DL-based tools hinders their application in nanopore selective sequencing. Here, we present a DL-based tool named ReadCurrent for nanopore selective sequencing, which takes electric currents as inputs. ReadCurrent employs a modified very deep convolutional neural network (VDCNN) architecture, enabling significantly lower computational costs for training and quicker inference compared to

SUBMITTER: Fan K 

PROVIDER: S-EPMC11370629 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature