Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.

ABSTRACT:

Background

RNA sequencing (RNA-seq) analyses can benefit from performing a genome-guided and de novo assembly, in particular for species where the reference genome or the annotation is incomplete. However, tools for integrating an assembled transcriptome with reference annotation are lacking.

Findings

Necklace is a software pipeline that runs genome-guided and de novo assembly and combines the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome out of the assembled and reference data. Reads are subsequently aligned and counted in preparation for differential expression testing.

Conclusions

Necklace allows a comprehensive transcriptome to be built from a combination of assembled and annotated tr

SUBMITTER: Davidson NM 

PROVIDER: S-EPMC5946861 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature