RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing.

Autor: de la Rubia I; EMBL Australia Partner Laboratory Network at the Australian National University, Acton, Canberra, ACT, 2601, Australia.; Pompeu Fabra University (UPF), E08003, Barcelona, Spain., Srivastava A; EMBL Australia Partner Laboratory Network at the Australian National University, Acton, Canberra, ACT, 2601, Australia.; Australian National University, Acton, Canberra, ACT, 2601, Australia., Xue W; EMBL Australia Partner Laboratory Network at the Australian National University, Acton, Canberra, ACT, 2601, Australia.; Australian National University, Acton, Canberra, ACT, 2601, Australia., Indi JA; EMBL Australia Partner Laboratory Network at the Australian National University, Acton, Canberra, ACT, 2601, Australia.; Universidade de Lisboa, Lisboa, Portugal., Carbonell-Sala S; Pompeu Fabra University (UPF), E08003, Barcelona, Spain.; Centre for Regulatory Genomics (CRG), E08001, Barcelona, Spain., Lagarde J; Pompeu Fabra University (UPF), E08003, Barcelona, Spain.; Centre for Regulatory Genomics (CRG), E08001, Barcelona, Spain., Albà MM; Pompeu Fabra University (UPF), E08003, Barcelona, Spain. malba@imim.es.; Catalan Institution for Research and Advanced Studies (ICREA), E08010, Barcelona, Spain. malba@imim.es.; Hospital del Mar Medical Research Institute (IMIM), E08001, Barcelona, Spain. malba@imim.es., Eyras E; EMBL Australia Partner Laboratory Network at the Australian National University, Acton, Canberra, ACT, 2601, Australia. eduardo.eyras@anu.edu.au.; Australian National University, Acton, Canberra, ACT, 2601, Australia. eduardo.eyras@anu.edu.au.; Catalan Institution for Research and Advanced Studies (ICREA), E08010, Barcelona, Spain. eduardo.eyras@anu.edu.au.; Hospital del Mar Medical Research Institute (IMIM), E08001, Barcelona, Spain. eduardo.eyras@anu.edu.au.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2022 Jul 08; Vol. 23 (1), pp. 153. Date of Electronic Publication: 2022 Jul 08.
DOI: 10.1186/s13059-022-02715-w
Abstrakt: Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes. Current methods for transcript identification and quantification rely on mapping reads to a reference genome, which precludes the study of species with a partial or missing reference or the identification of disease-specific transcripts not readily identifiable from a reference. We present RATTLE, a tool to perform reference-free reconstruction and quantification of transcripts using only Nanopore reads. Using simulated data and experimental data from isoform spike-ins, human tissues, and cell lines, we show that RATTLE accurately determines transcript sequences and their abundances, and shows good scalability with the number of transcripts.
(© 2022. The Author(s).)
Databáze: MEDLINE
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