Visualization and quality assessment of de novo genome assemblies.

Details

Ressource 1Download: BIB_78E4EA5A315D.P001.pdf (288.14 [Ko])
State: Public
Version: Final published version
Serval ID
serval:BIB_78E4EA5A315D
Type
Article: article from journal or magazin.
Collection
Publications
Title
Visualization and quality assessment of de novo genome assemblies.
Journal
Bioinformatics
Author(s)
Riba-Grognuz O., Keller L., Falquet L., Xenarios I., Wurm Y.
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Publication state
Published
Issued date
2011
Peer-reviewed
Oui
Volume
27
Number
24
Pages
3425-3426
Language
english
Abstract
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.Scripts that generate tables for visualization in Cytoscape from FASTA sequence and scaffolding information files are publicly available at https://github.com/ksanao/TGNet.
Keywords
De novo assembly, Networks, Quality assessment, Next-generation sequencing, Visualization
Pubmed
Web of science
Open Access
Yes
Create date
09/10/2011 20:05
Last modification date
20/08/2019 14:35
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