Extending rnaSPAdes functionality for hybrid transcriptome assembly

Andrey D. Prjibelski, Giuseppe D. Puglia, Dmitry Antipov, Elena Bushmanova, Daniela Giordano, Alla Mikheenko, Domenico Vitale, Alla Lapidus

Результат исследований: Научные публикации в периодических изданияхстатьярецензирование

Аннотация

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.

Язык оригиналаанглийский
Номер статьи302
Страницы (с-по)302
Число страниц9
ЖурналBMC Bioinformatics
Том21
Номер выпускаSuppl 12
DOI
СостояниеОпубликовано - 24 июл 2020

Предметные области Scopus

  • Прикладная математика
  • Молекулярная биология
  • Структурная биология
  • Биохимия
  • Прикладные компьютерные науки

Ключевые слова

  • transcriptomics
  • transcriptome assembly
  • RNA-Seq
  • Oxford nanopores
  • Iso-seq
  • Hybrid assembly
  • De novo assembly

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