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Genome Biol. 2019 Nov 29;20(1):260. doi: 10.1186/s13059-019-1884-z.

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

Author information

1
Pompeu Fabra University, E08003, Barcelona, Spain.
2
The John Curtin School of Medical, Australian National University, Acton ACT, Canberra, 2601, Australia.
3
EMBL Australia Partner Laboratory Network and the Australian National University, Acton ACT, Canberra, 2601, Australia.
4
Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
5
The John Curtin School of Medical, Australian National University, Acton ACT, Canberra, 2601, Australia. eduardo.eyras@anu.edu.au.
6
EMBL Australia Partner Laboratory Network and the Australian National University, Acton ACT, Canberra, 2601, Australia. eduardo.eyras@anu.edu.au.
7
IMIM - Hospital del Mar Medical Research Institute, E08003, Barcelona, Spain. eduardo.eyras@anu.edu.au.

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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