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bioRxiv · 10.1101/200287

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

Davidson, N. M.·Oshlack, A.
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Abstract

BackgroundRNA-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.\n\nFindingsNecklace 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.\n\nConclusionsNecklace 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 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.

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Davidson, N. M., Oshlack, A.. 2017-10-09. Necklace: combining reference and assembled transcriptomes for RNA-Seq analysis. https://doi.org/10.1101/200287

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