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

ABSTRACT:

Background

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 the organisms with finished and well-annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing, and paralogous genes.

Results

Herein we describe the novel transcriptome assembler rnaSPAdes, which has been developed on top of the SPAdes genome assembler and explores computational parallels between assembly of transcriptome

SUBMITTER: Bushmanova E 

PROVIDER: S-EPMC6736328 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature