Background: De novo genome assembly can be challenging due to inherent properties of the reads, even when using current state-of-the-art assembly tools based on de Bruijn graphs. Often users are not bio-informaticians and, in a black box approach, utilise assembly parameters such as contig length and N50 to generate whole genome sequences, potentially resulting in mis-assemblies. Findings. Utilising several assembly tools based on de Bruijn graphs like Velvet, SPAdes and IDBA, we demonstrate that at the optimal N50, mis-assemblies do occur, even when using the multi-k-mer approaches of SPAdes and IDBA. We demonstrate that whole genome mapping can be used to identify these mis-assemblies and can guide the selection of the best k-mer size which yields the highest N50 without mis-assemblies. Conclusions: We demonstrate the utility of whole genome mapping (WGM) as a tool to identify mis-assemblies and to guide k-mer selection and higher quality de novo genome assembly of bacterial genomes. © 2014 Xavier et al.; licensee BioMed Central Ltd.
CITATION STYLE
Xavier, B. B., Sabirova, J., Pieter, M., Hernalsteens, J. P., De Greve, H., Goossens, H., & Malhotra-Kumar, S. (2014). Employing whole genome mapping for optimal de novo assembly of bacterial genomes. BMC Research Notes, 7(1). https://doi.org/10.1186/1756-0500-7-484
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