rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

• Published in: Gigascience Vol. 8; no. 9
• Main Authors: Bushmanova, Elena, Antipov, Dmitry, Lapidus, Alla, Prjibelski, Andrey D
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 01.09.2019
• Subjects: Algorithms; Alternative splicing; Animals; Arabidopsis - genetics; Assembly; Caenorhabditis elegans - genetics; Computer applications; Datasets; Gene expression; Gene sequencing; Genes; Genomes; Humans; Isoforms; Mice; Quality assessment; Quality control; Ribonucleic acid; RNA; RNA-Seq; Splicing; Technical Note; Transcriptome; Transcriptomes; Transcriptomics; Zea mays - genetics; RNA-Seq; de novo assembly; transcriptome assembly

The possibility of generating large RNA-sequencing datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to...