Abstract
Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes from any sample. However, current methods for transcript identification and quantification rely of 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. Here 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. RATTLE provides unprecedented access to transcriptomes from any sample and species without relying on a reference or additional technologies.
Competing Interest Statement
E.E. has received support from Oxford Nanopore Technologies (ONT) to present the results from this manuscript at scientific conferences. However, ONT played no role in the algorithm or software developments, study design, analysis, or preparation of the manuscript.
Footnotes
We have performed additional benchmarking analyses and have clarified some of the algorithmic details.