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

Angel Ruiz-Reche; Akanksha Srivastava; Joel A Indi; Ivan de la Rubia; Eduardo Eyras

doi:10.1186/s13059-019-1884-z

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

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

Authors

Angel Ruiz-Reche¹, Akanksha Srivastava^{2

3}, Joel A Indi^{1

4}, Ivan de la Rubia¹, Eduardo Eyras^{5

6

7}

Affiliations

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. [email protected].
⁶ EMBL Australia Partner Laboratory Network and the Australian National University, Acton ACT, Canberra, 2601, Australia. [email protected].
⁷ IMIM - Hospital del Mar Medical Research Institute, E08003, Barcelona, Spain. [email protected].

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.

Publication types

Evaluation Study
Research Support, Non-U.S. Gov't

MeSH terms

DNA, Complementary / analysis*
Deep Learning*
Nanopore Sequencing*
Sequence Analysis, DNA*
Software*

Substances

DNA, Complementary