Scaffold Graph ToolKit (SGTK)  allows to construct and visualize scaffold graphs — graphs, vertices of which correspond to the assembled contigs and edges represent connections between them.  SGTK is able to construct scaffold graphs using different kinds of sequencing data: short paired reads, long noisy reads, assembled scaffolds, reference genomes, RNA-Seq data and transcript sequences. Thus, scaffolds graphs can be a useful instrument for analyzing and assessing genome assemblies. In addition, SGTK can scaffold genome assemblies using RNA-Seq data.