title: Employing whole genome mapping for optimal de novo assembly of bacterial genomes.
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.
  
  
  RESULTS
  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.
authors: Basil Britto
authors: BB
authors: Xavier
authors: Julia
authors: J
authors: Sabirova
authors: Moons
authors: M
authors: Pieter
authors: Jean-Pierre
authors: JP
authors: Hernalsteens
authors: Henri
authors: H
authors: de Greve
authors: Herman
authors: H
authors: Goossens
authors: Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium. surbhi.malhotra@uantwerpen.be.
authors: Surbhi
authors: S
authors: Malhotra-Kumar
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D020451:Contig Mapping; D016680:Genome, Bacterial / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software; D013211:Staphylococcus aureus / Q000235:genetics*