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

Dataset type: Transcriptomic, Software, Workflow
Data released on April 13, 2018

Davidson NM; Oshlack A (2018): Supporting data for "Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis" GigaScience Database. http://dx.doi.org/10.5524/100438

DOI10.5524/100438

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 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 RNAseq data is mapped back to this newly created superTranscript reference to enable differential expression testing with standard methods. Necklace is available from https://github.com/Oshlack/necklace/wiki under GPL 3.0.

Additional details

Read the peer-reviewed publication(s):

Davidson, N. M., & Oshlack, A. (2018). Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis. GigaScience, 7(5). doi:10.1093/gigascience/giy045

Additional information:

https://github.com/Oshlack/necklace/wiki

https://scicrunch.org/resolver/RRID:SCR_016103





File NameSample IDData TypeFile FormatSizeRelease Date 
GitHub archivearchive29.72 KB2018-03-30
ReadmeTEXT1.56 KB2018-03-30
Displaying 1-2 of 2 File(s).
Funding body Awardee Award ID Comments
National Health and Medical Research Council A Oshlack GNT1126157
Date Action
April 13, 2018 Dataset publish
July 9, 2018 Manuscript Link added : 10.1093/gigascience/giy045