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Necklace is design to replace many manual steps in the pipeline of RNA-Seq analyses involving species with incomplete genome or annotations. ie. most organisms other than human, mouse, drosophila etc. In such species, RNA-Seq analyses can benefit from performing a genome-guided and de novo assembly, in addition to using the reference annotation. Necklace is a bpipe pipeline to run both types of assembly and combine the resulting transcriptomes with reference genome annotations. It will constructs a compact but comprehensive superTranscriptome (see our superTranscriptome paper about the Lace assembler). Reads are subsequently aligned and counted in preparation for differential gene expression testing and isoform usage analysis.

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, https://doi.org/10.1093/gigascience/giy045