title: Visualization and quality assessment of de novo genome assemblies.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  oksana.ribagrognuz@unil.ch; yannick.wurm@unil.ch
  
  
  BACKGROUND
  Scripts that generate tables for visualization in Cytoscape from FASTA sequence and scaffolding information files are publicly available at https://github.com/ksanao/TGNet.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland. oksana.ribagrognuz@unil.ch
authors: Oksana
authors: O
authors: Riba-Grognuz
authors: Laurent
authors: L
authors: Keller
authors: Laurent
authors: L
authors: Falquet
authors: Ioannis
authors: I
authors: Xenarios
authors: Yannick
authors: Y
authors: Wurm
mesh_terms: D002874:Chromosome Mapping; D019295:Computational Biology; D016678:Genome; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D026801:Synteny