Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis
Nadia M Davidson, Alicia Oshlack
GigaScience | OXFORD UNIV PRESS | Published : 2018
Background: RNA sequencing (RNA-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 an assembled transcriptome with reference annotation are lacking. Findings: Necklace 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. Conclusions: Necklace allows a compreh..View full abstract
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Awarded by National Health and Medical Reseach Council
A.O. is funded by an National Health and Medical Reseach Council, Career Development Fellowship GNT1126157.