Employing whole genome mapping for optimal de novo assembly of bacterial genomes

BMC Research Notes

Surbhi Malhotra-Kumar²  Herman Goossens²  Henri de Greve³  Jean-Pierre Hernalsteens¹  Moons Pieter²  Julia Sabirova²  Basil Britto Xavier² 

[1] Viral Genetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium;Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium;Structural Biology Brussels, Flanders Institute for Biotechnology (VIB), Vrije Universiteit Brussel, Brussels, Belgium

关键词: SPAdes and Velvet;    de bruijn graph;    Microbial genomes;    k-mer;    Whole genome mapping;    De-novo assembly;   

Others  :  1131786
DOI  :  10.1186/1756-0500-7-484

 received in 2014-04-08, accepted in 2014-07-21,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Xavier et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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