Scripture makes use of aligned reads to the genome. As such, the quality of the transcriptome reconstruction is highly dependent on the quality of the aligner used. It is critical to use a spliced aligner, an aligner that can map reads across exon-exon junctions. Scripture is agnostic to the exact aligner used.
A few examples of available spliced aligners:
NOTE: In our experience, Tophat works quite well as input for the Scripture method and is currently our aligner of choice. However, we have not done a comprehensive comparison of other gapped aligners.