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

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

Blog Article

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 Samsung RR39M7140WW RR7000M A+ Free Standing Larder Fridge 385 Litres White disease-specific transcripts not readily identifiable from a reference.We present RATTLE, a Baby Jumpers 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.