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Oksana Riba-Grognuz, Laurent Keller, Laurent Falquet, Ioannis Xenarios and Yannick Wurm (Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland; Swiss Institute for Bioinformatics, University of Lausanne, Lausanne, Switzerland)Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality of such assemblies is critical for subsequent analysis. We present a method to evaluate genome scaffolding by aligning independently obtained transcriptome sequences to the genome and visually summarizing the alignments using the Cytoscape software. Applying this method to the genome of the red fire ant Solenopsis invicta allowed us to identify inconsistencies in 7%, confirm contig order in 20% and extend 16% of scaffolds.