Fig. 6.

Ryūtō, Scallop, and StringTie allow the use of aligned de novo assembled super-reads next to normal paired-end alignments, all showing improvements when using this method, both using the more accurate HISAT (l.h.s.) or to a lesser degree STAR (r.h.s.) for de novo alignment. Combined alignments were run in standard setting (up-pointing triangle) as well as with filter coverage 5 (left-pointing triangle)