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Title
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Employing whole genome mapping for optimal de novo assembly of bacterial genomes
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Author
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Abstract
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| 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. |
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Language
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English
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Source (journal)
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BMC research notes
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Publication
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2014
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ISSN
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1756-0500
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DOI
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10.1186/1756-0500-7-484
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Volume/pages
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7
(2014)
, 4 p.
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Article Reference
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484
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Medium
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E-only publicatie
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Full text (Publisher's DOI)
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Full text (open access)
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