De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers.

ABSTRACT:

Background

In recent years, massively parallel complementary DNA sequencing (RNA sequencing [RNA-Seq]) has emerged as a fast, cost-effective, and robust technology to study entire transcriptomes in various manners. In particular, for non-model organisms and in the absence of an appropriate reference genome, RNA-Seq is used to reconstruct the transcriptome de novo. Although the de novo transcriptome assembly of non-model organisms has been on the rise recently and new tools are frequently developing, there is still a knowledge gap about which assembly software should be used to build a comprehensive de novo assembly.

Results

Here, we present a large-scale comparative study in which 10 de novo assembly tools are applied to 9 RNA-Seq data sets spanning different kingdoms of lif

SUBMITTER: Holzer M 

PROVIDER: S-EPMC6511074 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature