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In species where the reference genome or annotation is incomplete, RNA-Seq analyses can benefit from performing a genome-guided and de novo assembly, in addition to using the reference annotation. Necklace is a software pipeline to run genome-guided and de novo assembly and combine the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome (see out of the assembled and reference data. Reads are subsequently aligned and counted in preparation for differential gene expression testing and isoform usage analysis.

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Citation: Nadia M Davidson, Alicia Oshlack, Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis, GigaScience, Volume 7, Issue 5, May 2018, giy045,

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