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Updated: May 28, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
Visualization and quality assessment of de novo genome assemblies
Oksana Riba-Grognuz1, Laurent Keller, Laurent Falquet
1Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland. oksana.ribagrognuz@unil.ch
Summary:
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.
Contact:
oksana.ribagrognuz@unil.ch; yannick.wurm@unil.ch
Availability:
Scripts that generate tables for visualization in Cytoscape from FASTA sequence and scaffolding information files are publicly available at https://github.com/ksanao/TGNet.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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