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 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1284-1) out of the assembled and reference data. Reads are subsequently aligned and counted in preparation for differential gene expression testing and isoform usage analysis.
Please see https://github.com/Oshlack/necklace/wiki for more information