Title
Employing whole genome mapping for optimal de novo assembly of bacterial genomes Employing whole genome mapping for optimal de novo assembly of bacterial genomes
Author
Faculty/Department
Faculty of Sciences. Biology
Faculty of Medicine and Health Sciences
Publication type
article
Publication
Subject
Human medicine
Source (journal)
BMC research notes
Volume/pages
7(2014) , p. 1-4
ISSN
1756-0500
Article Reference
484
Carrier
E-only publicatie
Target language
English (eng)
Full text (Publishers DOI)
Affiliation
University of Antwerp
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.
Full text (open access)
https://repository.uantwerpen.be/docman/irua/92070c/5fffda02.pdf
Handle