1. Bioinformatics. 2011 Oct 12. [Epub ahead of print]

Visualization and quality assessment of de novo genome assemblies.

Riba-Grognuz O, Keller L, Falquet L, Xenarios I, Wurm Y.

Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne,
Switzerland.

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.


PMID: 21994228  [PubMed - as supplied by publisher]