Abstract
Motivation: RNA-Seq analyses can benefit from performing a genome-guided and de novo assem- bly, in particular for species where the reference genome is incomplete. However, tools to integrate assembled transcriptome with reference annotation are lacking.
Results: 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 out of the assembled and reference data. Reads are subse-quently aligned and counted in preparation for differential expression testing.
Availability: Necklace is available from https://github.com/Oshlack/necklace/wiki under GPL 3.0.
Contact: nadia.davidson{at}mcri.edu.au or alicia.oshlack{at}mcri.edu.au
Supplementary information: Supplementary methods are available at Bioinformatics online.