ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning.

ABSTRACT: We describe ReorientExpress, a method to perform reference-free orientation of transcriptomic long sequencing reads. ReorientExpress uses deep learning to correctly predict the orientation of the majority of reads, and in particular when trained on a closely related species or in combination with read clustering. ReorientExpress enables long-read transcriptomics in non-model organisms and samples without a genome reference without using additional technologies and is available at https://github.com/comprna/reorientexpress.

SUBMITTER: Ruiz-Reche A 

PROVIDER: S-EPMC6883653 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature