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BMC Res Notes. 2014 Jul 30;7:484. doi: 10.1186/1756-0500-7-484.

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

Author information

1
Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium. surbhi.malhotra@uantwerpen.be.

Abstract

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.

PMID:
25077983
PMCID:
PMC4118782
DOI:
10.1186/1756-0500-7-484
[Indexed for MEDLINE]
Free PMC Article

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