Extending rnaSPAdes functionality for hybrid transcriptome assembly

BMC Bioinformatics

Elena Bushmanova¹  Andrey D. Prjibelski¹  Alla Lapidus¹  Alla Mikheenko¹  Dmitry Antipov¹  Giuseppe D. Puglia²  Domenico Vitale²  Daniela Giordano³ 

[1] Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University;Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo;Department of Electrical, Electronics and Computer Engineering, University of Catania;

关键词: Transcriptome assembly;    Hybrid assembly;    De novo assembly;    Transcriptomics;    RNA-Seq;    Iso-seq;   

DOI  :  10.1186/s12859-020-03614-2

来源: DOAJ

【 摘 要 】

Abstract Background De novo RNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impossible to reconstruct complete sequences of complex genes and alternative isoforms. Recently emerged possibility to generate long RNA reads, such as PacBio and Oxford Nanopores, may dramatically improve the assembly quality, and thus the consecutive analysis. While reference-based tools for analysing long RNA reads were recently developed, there is no established pipeline for de novo assembly of such data. Results In this work we present a novel method that allows to perform high-quality de novo transcriptome assemblies by combining accuracy and reliability of short reads with exon structure information carried out from long error-prone reads. The algorithm is designed by incorporating existing hybridSPAdes approach into rnaSPAdes pipeline and adapting it for transcriptomic data. Conclusion To evaluate the benefit of using long RNA reads we selected several datasets containing both Illumina and Iso-seq or Oxford Nanopore Technologies (ONT) reads. Using an existing quality assessment software, we show that hybrid assemblies performed with rnaSPAdes contain more full-length genes and alternative isoforms comparing to the case when only short-read data is used.

【 授权许可】

Unknown