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

Autor: Ruiz-Reche A; Pompeu Fabra University, E08003, Barcelona, Spain., Srivastava A; The John Curtin School of Medical, Australian National University, Acton ACT, Canberra, 2601, Australia.; EMBL Australia Partner Laboratory Network and the Australian National University, Acton ACT, Canberra, 2601, Australia., Indi JA; Pompeu Fabra University, E08003, Barcelona, Spain.; Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal., de la Rubia I; Pompeu Fabra University, E08003, Barcelona, Spain., Eyras E; The John Curtin School of Medical, Australian National University, Acton ACT, Canberra, 2601, Australia. eduardo.eyras@anu.edu.au.; EMBL Australia Partner Laboratory Network and the Australian National University, Acton ACT, Canberra, 2601, Australia. eduardo.eyras@anu.edu.au.; IMIM - Hospital del Mar Medical Research Institute, E08003, Barcelona, Spain. eduardo.eyras@anu.edu.au.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2019 Nov 29; Vol. 20 (1), pp. 260. Date of Electronic Publication: 2019 Nov 29.
DOI: 10.1186/s13059-019-1884-z
Abstrakt: 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.
Databáze: MEDLINE
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