Vaccinium virgatum transcriptome
DNA from leaves, green berries, and bud tips from Vaccinium virgatum cv. Premier were sequenced and assembled. The manuscript is currently in preparation. Data was provided pre-publication by Miriam Paya-Milans and Meg Staton from the University of Tennessee, Knoxville. Also see the expression analysis project page.
NCBI Biomaterial Accessions:
Two settings of k-mer 25 and k-mer 31 were applied in Trinity de novo assembly, and default settings on genome guided assembly. k-mer range of 25 to 55 with a step size of 10 were used in SOAPdenovo-Trans, TransABySS and velvet. To remove the redundancy on Trinity and SOAPdenovo-Trans, all contigs were pooled by software and clustered using CD-HIT-EST v4.6.6 with 95% identity. On velvet and TransABySS, reduced assemblies were obtained with Oases and transabyss-merge, respectively. The result of the four programs were pooled and reduced with CD-HIT to obtain the final transcriptome.
Additional information about this analysis: