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

Ruiz Reche, Angel; Srivastava, Akanksha; Indi, Joel A.; de la Rubia, Ivan; Eyras Jiménez, Eduardo

doi:http://dx.doi.org/10.1186/s13059-019-1884-z

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

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Ruiz-Reche A, Srivastava A, Indi JA, de la Rubia I, Eyras E. ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning. Genome Biol. 2019; 20(1):260. DOI: 10.1186/s13059-019-1884-z

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.