Lamm, et al, reported that a published application note shows the supremacy of circularizing ssDNA templates for Illumina-based sequencing. They noted that they saw great advantages to using CircLigase-based and ssRNA-based capture for defining the sequences and structures of the precise 5´ ends. This information was lost when they used a double-strand cDNA capture method. This paper, which is cited below, compares sequencing RNA templates using three different templates generated using CircLigase and T4 RNA Ligase.
Lamm, A. T., et al. (2011) Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome. Genome Res. 21:2, 265-275. Doi: 10.1101/gr.108845.110.