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

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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.

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Ruiz-Reche, A., Srivastava, A., Indi, J. A., De La Rubia, I., & Eyras, E. (2019). ReorientExpress: Reference-free orientation of nanopore cDNA reads with deep learning. Genome Biology, 20(1). https://doi.org/10.1186/s13059-019-1884-z

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