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

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. Necklace is a sof...

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Bibliographic Details
Published in:Gigascience 2018-05, Vol.7 (5)
Main Authors: Davidson, Nadia M, Oshlack, Alicia
Format: Article
Language:English
Subjects:
Animals
Annotations
Assembly
Databases, Genetic
Gene sequencing
Genomes
Molecular Sequence Annotation
Reference Standards
Ribonucleic acid
RNA
RNA, Messenger - genetics
RNA, Messenger - metabolism
Sequence Analysis, RNA - methods
Sheep - genetics
Software
Technical Note
Transcriptome - genetics
Transcriptomes
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Summary: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. 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. Necklace allows a comprehensive transcriptome to be built from a combination of assembled and annotated transcripts, which results in a more comprehensive transcriptome for the majority of organisms. In addition RNA-seq data are mapped back to this newly created superTranscript reference to enable differential expression testing with standard methods.
ISSN:2047-217X
2047-217X
DOI:10.1093/gigascience/giy045