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

Rubia, Ivan de la; Srivastava, Akanksha; Xue, Wenjing; Indi, Joel A.; Carbonell Sala, Silvia; Lagarde, Julien; Albà Soler, Mar; Eyras Jiménez, Eduardo

doi:http://dx.doi.org/10.1186/s13059-022-02715-w

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

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de la Rubia I, Srivastava A, Xue W, Indi JA, Carbonell-Sala S, Lagarde J, Albà MM, Eyras E. RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing. Genome Biol. 2022 Jul 8;23(1):153. DOI: 10.1186/s13059-022-02715-w

Abstract

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.